diff --git a/core.json b/core.json index cbd70634..a801c5ff 100644 --- a/core.json +++ b/core.json @@ -7,12 +7,12 @@ "val" : "https://creativecommons.org/publicdomain/zero/1.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : "https://github.com/oborel/obo-relations/wiki/ROCore" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/core.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/core.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", diff --git a/core.obo b/core.obo index 5ef0e65d..ef9d44e4 100644 --- a/core.obo +++ b/core.obo @@ -1,9 +1,9 @@ format-version: 1.2 -data-version: ro/releases/2023-08-18/core.owl +data-version: ro/releases/2024-02-13/core.owl ontology: ro/core property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage "https://github.com/oborel/obo-relations/wiki/ROCore" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Term] id: BFO:0000002 @@ -381,8 +381,8 @@ property_value: IAO:0000116 "Location as a relation between instances: The primi property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true [Typedef] diff --git a/core.owl b/core.owl index 5604e8b3..89595aca 100644 --- a/core.owl +++ b/core.owl @@ -13,9 +13,9 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2023-08-18 + 2024-02-13 https://github.com/oborel/obo-relations/wiki/ROCore @@ -985,5 +985,5 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + diff --git a/ro-base.json b/ro-base.json index f82d0759..25a78385 100644 --- a/ro-base.json +++ b/ro-base.json @@ -16,12 +16,12 @@ "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro-base.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -1195,12 +1195,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -3975,7 +3980,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -4192,11 +4197,11 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002310", - "lbl" : "exposure event or process", + "lbl" : "obsolete exposure event or process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." + "val" : "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -4219,7 +4224,8 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" - } ] + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002312", @@ -8861,6 +8867,43 @@ "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", @@ -10533,6 +10576,54 @@ "val" : "2022-09-26T06:08:01Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11017,6 +11108,25 @@ "val" : "https://orcid.org/0000-0003-1909-9269" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017005", + "lbl" : "contains measured amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2999-0103" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-5714-991X" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -11428,6 +11538,63 @@ "val" : "https://orcid.org/0000-0002-4142-7153" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -13500,10 +13667,6 @@ "sub" : "http://purl.obolibrary.org/obo/CHEBI_50906", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002310", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002532", "pred" : "http://purl.obolibrary.org/obo/RO_0002524", @@ -13908,6 +14071,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -15380,6 +15547,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -15792,6 +15967,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -15968,6 +16151,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -16644,6 +16843,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003000", "pred" : "inverseOf", @@ -16974,7 +17177,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -17286,10 +17489,26 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0017005", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000967" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000121" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/ro-base.obo b/ro-base.obo index 8efea67c..f5733cdf 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: ro/releases/2023-08-18/ro-base.owl +data-version: ro/releases/2024-02-13/ro-base.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -12,7 +12,7 @@ property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Term] id: BFO:0000002 @@ -128,14 +128,14 @@ id: GO:0019107 [Term] id: RO:0002310 -name: exposure event or process -def: "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] -is_a: BFO:0000015 ! process +name: obsolete exposure event or process +def: "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/pull/173" xsd:anyURI +is_obsolete: true created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:55:39Z @@ -612,8 +612,8 @@ property_value: IAO:0000116 "Most location relations will only hold at certain t property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true transitive_over: BFO:0000050 ! part of @@ -722,8 +722,10 @@ is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 -name: regulates in other organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 ! process range: BFO:0000015 ! process @@ -1270,7 +1272,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -1450,7 +1452,7 @@ def: "a is attached to part of b if a is attached to b, or a is attached to some property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string domain: UBERON:0000061 range: UBERON:0000061 -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1516,6 +1518,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -1702,7 +1705,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -1742,7 +1745,7 @@ def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1980,7 +1983,7 @@ id: RO:0002244 name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 ! exposure event or process +domain: COB:0001000 is_a: RO:0002410 ! causally related to [Typedef] @@ -2219,7 +2222,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 -name: results in formation of +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -2367,7 +2370,7 @@ property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -2484,7 +2487,7 @@ name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -2768,7 +2771,7 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3191,7 +3194,7 @@ property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd: property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -3625,7 +3628,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 @@ -3859,7 +3862,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system range: BFO:0000040 ! material entity -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -4110,7 +4113,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of is_asymmetric: true @@ -4370,7 +4373,7 @@ is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results in synthesis of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 @@ -4378,7 +4381,7 @@ name: results in assembly of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] @@ -4679,6 +4682,26 @@ property_value: IAO:0000119 Communal:roosting is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with +[Typedef] +id: RO:0002802 +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: RO:0002454 ! has host + [Typedef] id: RO:0003000 name: produces @@ -5613,6 +5636,28 @@ is_a: RO:0012011 ! indirectly causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z +[Typedef] +id: RO:0012013 +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + +[Typedef] +id: RO:0012014 +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: RO:0013001 name: has synaptic IO in region @@ -5869,6 +5914,16 @@ property_value: IAO:0000118 "inversely correlated with" xsd:string is_symmetric: true is_a: RO:0002610 ! correlated with +[Typedef] +id: RO:0017005 +name: contains measured amount +def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2999-0103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-5714-991X +property_value: IAO:0000112 "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." xsd:string +domain: OBI:0000967 +range: COB:0000121 + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -5988,7 +6043,7 @@ synonym: "is desmotrope of" EXACT [] xref: obo:chebi#is_tautomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38707", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38709"} +property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {seeAlso="CHEBI:38707", seeAlso="CHEBI:38709"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6000,7 +6055,7 @@ def: "Group A is a substituent group from Chemical B if A represents the functio xref: obo:chebi#is_substituent_group_from property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:30795", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:58957"} +property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {seeAlso="CHEBI:30795", seeAlso="CHEBI:58957"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6011,7 +6066,7 @@ def: "Chemical A has functional parent Chemical B if there is chemical transform xref: obo:chebi#has_functional_parent property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50851", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50854"} +property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {seeAlso="CHEBI:50851", seeAlso="CHEBI:50854"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6023,7 +6078,7 @@ synonym: "is optical isomer of" EXACT [] xref: obo:chebi#is_enantiomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:31472"} +property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", seeAlso="CHEBI:31472"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6035,7 +6090,7 @@ def: "Chemical A has parent hydride Chemical B if there exists a molecular graph xref: obo:chebi#has_parent_hydride property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:39106", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:52083"} +property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {seeAlso="CHEBI:39106", seeAlso="CHEBI:52083"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6073,6 +6128,40 @@ def: "Relates a gene to condition, such that a variation in this gene predispose is_a: RO:0003304 ! contributes to condition created_by: https://orcid.org/0000-0002-4142-7153 +[Typedef] +id: RO:0020101 +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: RO:0002178 ! supplies + +[Typedef] +id: RO:0020102 +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: RO:0002179 ! drains + +[Typedef] +id: RO:0020103 +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: RO:0002178 ! supplies +is_a: RO:0002179 ! drains + [Typedef] id: RO:0040035 name: disease relationship diff --git a/ro-base.owl b/ro-base.owl index f6602b63..b64dfefc 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -18,12 +18,12 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2023-08-18 + 2024-02-13 https://github.com/oborel/obo-relations/ @@ -1994,7 +1994,9 @@ AND t has_input y x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - regulates in other organism + regulates in other organism + + regulates in another organism @@ -3329,6 +3331,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + @@ -4079,7 +4082,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to @@ -4446,7 +4449,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results in formation of + results in formation of anatomical entity @@ -8339,6 +8342,34 @@ the a supports either the existence of b, or the truth value of b. + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -9805,6 +9836,36 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + positively regulates in other organism + + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + negatively regulates in other organism + + negatively regulates in another organism + + + + @@ -10246,6 +10307,20 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. + A relation between a container and measurement datum that specifies the actual amount of material in the container. + + + contains measured amount + + + + @@ -10616,6 +10691,52 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + directly supplies and drains + + + + @@ -12563,6 +12684,18 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + + + + + + @@ -12632,6 +12765,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + @@ -12671,16 +12810,16 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. + OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. 2017-06-05T17:55:39Z - exposure event or process + obsolete exposure event or process https://github.com/oborel/obo-relations/pull/173 + true @@ -12768,6 +12907,18 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + + + + + + @@ -12909,10 +13060,10 @@ binary, and takes no temporal argument. /////////////////////////////////////////////////////////////////////////////////////// --> - + - + @@ -12930,66 +13081,54 @@ binary, and takes no temporal argument. - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - @@ -13002,8 +13141,8 @@ binary, and takes no temporal argument. - - + + @@ -13013,7 +13152,7 @@ binary, and takes no temporal argument. - + @@ -13023,7 +13162,7 @@ binary, and takes no temporal argument. - + @@ -13040,8 +13179,8 @@ binary, and takes no temporal argument. - - + + @@ -13303,7 +13442,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13313,8 +13452,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13324,8 +13463,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13342,8 +13481,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13362,7 +13501,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13372,8 +13511,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13383,8 +13522,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13401,8 +13540,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13419,8 +13558,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13430,7 +13569,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13440,8 +13579,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13451,8 +13590,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13471,8 +13610,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13490,8 +13629,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13501,8 +13640,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13512,8 +13651,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13530,8 +13669,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13548,8 +13687,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13559,8 +13698,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13570,8 +13709,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13588,8 +13727,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13606,8 +13745,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13617,8 +13756,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13628,8 +13767,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13646,8 +13785,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13664,8 +13803,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13675,8 +13814,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13691,8 +13830,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13709,8 +13848,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13720,8 +13859,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13736,8 +13875,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13754,8 +13893,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13765,8 +13904,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13781,8 +13920,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13799,8 +13938,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13810,8 +13949,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13826,8 +13965,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13844,8 +13983,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13855,8 +13994,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13871,8 +14010,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13889,8 +14028,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13900,8 +14039,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13916,7 +14055,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13926,7 +14065,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13945,8 +14084,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13956,8 +14095,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13972,7 +14111,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13982,7 +14121,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14044,8 +14183,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -14055,8 +14194,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -14071,8 +14210,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -14088,8 +14227,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -14098,9 +14237,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -14114,9 +14253,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -14132,8 +14271,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -14142,9 +14281,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -14158,7 +14297,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14259,5 +14398,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/ro-full.json b/ro-full.json index ecabec35..3d4c0d6e 100644 --- a/ro-full.json +++ b/ro-full.json @@ -13,12 +13,12 @@ "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro-full.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -153,7 +153,14 @@ "definition" : { "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" }, - "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ] + "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/OBOFoundry/COB/issues/65" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", @@ -459,10 +466,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", - "xrefs" : [ "CARO:mah" ] + "val" : "A material entity that has a plasma membrane and results from cellular division." }, - "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], + "comments" : [ "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.", "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).", "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism." ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -536,6 +542,19 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/COB_0000121", + "lbl" : "measurement datum", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/COB_0001000", + "lbl" : "exposure of organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process during which an organism comes into contact with another entity." + } + } }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", "lbl" : "environmental system", @@ -596,7 +615,7 @@ "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", "xrefs" : [ "GOC:pdt" ] }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], + "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "This is the same as GO molecular function" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecular function" @@ -924,10 +943,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", - "xrefs" : [ "GOC:pdt" ] + "val" : "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." }, - "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological process" @@ -2273,6 +2291,84 @@ "val" : "EL++ ontology module" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000047", + "lbl" : "processed material", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Is a material entity that is created or changed during material processing." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "processed material" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000967", + "lbl" : "container", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A device that can be used to restrict the location of material entities over time" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "container" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000123" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000968", + "lbl" : "device", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "device" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A voltmeter is a measurement device which is intended to perform some measure function." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Helen Parkinson" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "instrument" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI development call 2012-12-17." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0100026", "lbl" : "organism", @@ -2625,6 +2721,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -3359,12 +3458,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -6139,7 +6243,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -6356,11 +6460,11 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002310", - "lbl" : "exposure event or process", + "lbl" : "obsolete exposure event or process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." + "val" : "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -6383,7 +6487,8 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" - } ] + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002312", @@ -11025,6 +11130,43 @@ "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", @@ -12697,6 +12839,54 @@ "val" : "2022-09-26T06:08:01Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -13181,6 +13371,25 @@ "val" : "https://orcid.org/0000-0003-1909-9269" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017005", + "lbl" : "contains measured amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2999-0103" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-5714-991X" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -13592,6 +13801,63 @@ "val" : "https://orcid.org/0000-0002-4142-7153" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -15527,8 +15793,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -15586,8 +15850,6 @@ } ], "xrefs" : [ { "val" : "CARO:0001001" - }, { - "val" : "FBbt:00005099" }, { "val" : "NLX:147821" } ] @@ -15612,8 +15874,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -15658,8 +15918,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -15693,6 +15951,8 @@ "val" : "AAO:0010841" }, { "val" : "AEO:0000000" + }, { + "val" : "BFO:0000004" }, { "val" : "BILA:0000000" }, { @@ -15701,8 +15961,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -15732,6 +15990,143 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "lbl" : "blood vessel", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vessel through which blood circulates in the body.", + "xrefs" : [ "BTO:0001102", "Wikipedia:Blood_vessel" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "vascular element", + "xrefs" : [ "EMAPA:35993" ] + }, { + "pred" : "hasExactSynonym", + "val" : "region of vascular tree organ", + "xrefs" : [ "FMA:50722" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vascular tree organ region", + "xrefs" : [ "FMA:50722" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011004" + }, { + "val" : "AEO:0000207" + }, { + "val" : "BTO:0001102" + }, { + "val" : "CALOHA:TS-0080" + }, { + "val" : "EFO:0000817" + }, { + "val" : "EHDAA2:0003252" + }, { + "val" : "EHDAA:240" + }, { + "val" : "EMAPA:32743" + }, { + "val" : "EMAPA:35993" + }, { + "val" : "FMA:50722" + }, { + "val" : "FMA:63183" + }, { + "val" : "GAID:169" + }, { + "val" : "MA:0000060" + }, { + "val" : "MAT:0000393" + }, { + "val" : "MESH:D001808" + }, { + "val" : "NCIT:C12679" + }, { + "val" : "NLXANAT:090901" + }, { + "val" : "SCTID:361097006" + }, { + "val" : "TAO:0002137" + }, { + "val" : "UMLS:C0005847" + }, { + "val" : "VHOG:0001250" + }, { + "val" : "Wikipedia:Blood_vessel" + }, { + "val" : "XAO:0001011" + }, { + "val" : "ZFA:0005314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001982", + "lbl" : "capillary", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any of the smallest blood vessels connecting arterioles with venules.", + "xrefs" : [ "ISBN:0073040584", "Wikipedia:Capillary", "https://github.com/obophenotype/uberon/issues/137" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blood capillary" + }, { + "pred" : "hasExactSynonym", + "val" : "capillary vessel" + } ], + "xrefs" : [ { + "val" : "AAO:0010252" + }, { + "val" : "BTO:0002045" + }, { + "val" : "CALOHA:TS-2006" + }, { + "val" : "EFO:0001906" + }, { + "val" : "EMAPA:35198" + }, { + "val" : "EV:0100035" + }, { + "val" : "FMA:63194" + }, { + "val" : "MA:0000065" + }, { + "val" : "MESH:D002196" + }, { + "val" : "NCIT:C12685" + }, { + "val" : "NLXANAT:090902" + }, { + "val" : "TAO:0005250" + }, { + "val" : "UMLS:C0935624" + }, { + "val" : "VHOG:0001253" + }, { + "val" : "Wikipedia:Capillary" + }, { + "val" : "XAO:0000116" + }, { + "val" : "ZFA:0005250" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2186" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", "lbl" : "multicellular anatomical structure", @@ -15749,8 +16144,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -15938,6 +16331,16 @@ "val" : "is defined by" } ] } + }, { + "id" : "https://orcid.org/0000-0001-6677-8489", + "lbl" : "Aleix Puig-Barbé", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0001-6677-8489" + } ] + } }, { "id" : "https://orcid.org/0000-0001-6996-0040", "lbl" : "Austin Meier", @@ -15978,6 +16381,16 @@ "val" : "data scientist" } ] } + }, { + "id" : "https://orcid.org/0000-0002-2999-0103", + "lbl" : "Jie Zheng", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-2999-0103)" + } ] + } }, { "id" : "https://orcid.org/0000-0002-4366-3088", "lbl" : "Pier Luigi Buttigieg", @@ -15988,6 +16401,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-5714-991X", + "lbl" : "Christian J Stoeckert", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-6601-2165", "lbl" : "Christopher J. Mungall", @@ -16048,6 +16471,26 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1813-6857", + "lbl" : "Pascale Gaudet", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Canadian biocurator" + } ] + } + }, { + "id" : "https://orcid.org/0000-0003-1909-9269", + "lbl" : "S. Clint Dowland", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-1909-9269" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1940-6740", "lbl" : "Anna Maria Masci", @@ -16058,6 +16501,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-3138-4118", + "lbl" : "Jorrit Poelen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "software/data engineer" + } ] + } }, { "id" : "https://orcid.org/0000-0003-4423-4370", "lbl" : "Charles Tapley Hoyt", @@ -16133,6 +16586,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000540", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/COB_0001000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", @@ -16141,10 +16598,26 @@ "sub" : "http://purl.obolibrary.org/obo/ENVO_01000739", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0003674", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0004842", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0003674" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0005634", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0008150", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0008150", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0003674" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0016301", "pred" : "is_a", @@ -16157,6 +16630,18 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000030", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000047", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000967", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000968" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000968", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000047" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0100026", "pred" : "is_a", @@ -16181,10 +16666,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002124", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002310", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002532", "pred" : "http://purl.obolibrary.org/obo/RO_0002524", @@ -16229,6 +16710,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010000" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001982", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010000", "pred" : "is_a", @@ -16633,6 +17122,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -18105,6 +18598,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -18517,6 +19018,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -18693,6 +19202,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -19369,6 +19894,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003000", "pred" : "inverseOf", @@ -19468,6 +19997,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -19507,6 +20040,13 @@ "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -19525,7 +20065,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", @@ -19533,7 +20073,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", @@ -19699,7 +20239,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -20011,10 +20551,26 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0017005", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000967" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000121" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/ro-full.obo b/ro-full.obo index 6879f323..5d3d9956 100644 --- a/ro-full.obo +++ b/ro-full.obo @@ -1,19 +1,24 @@ format-version: 1.2 -data-version: ro/releases/2023-08-18/ro-full.owl +data-version: ro/releases/2024-02-13/ro-full.owl subsetdef: common_anatomy "" +subsetdef: efo_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: human_reference_atlas "" +subsetdef: pheno_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" +subsetdef: uberon_slim "" subsetdef: upper_level "" +subsetdef: vertebrate_core "" ontology: ro/ro-full property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Term] id: BFO:0000002 @@ -37,7 +42,7 @@ name: independent continuant def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000020 ! characteristic disjoint_from: BFO:0000031 ! generically dependent continuant relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant @@ -52,6 +57,7 @@ name: process def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000015 {all_only="true"} ! part of process relationship: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process [Term] @@ -62,26 +68,31 @@ disjoint_from: BFO:0000023 ! role [Term] id: BFO:0000017 +name: realizable name: realizable entity def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic disjoint_from: BFO:0000019 ! quality relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity [Term] id: BFO:0000019 name: quality -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 +name: characteristic name: specifically dependent continuant def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of characteristic +relationship: BFO:0000051 BFO:0000020 {all_only="true"} ! has part characteristic +property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string [Term] id: BFO:0000023 @@ -122,7 +133,10 @@ is_a: PATO:0000001 ! quality id: CL:0000000 name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] +def: "A material entity that has a plasma membrane and results from cellular division." [] +comment: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). +comment: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. xref: CALOHA:TS-2035 xref: FBbt:00007002 xref: FMA:68646 @@ -160,6 +174,16 @@ xref: WBbt:0003679 is_a: CL:0000000 ! cell property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: COB:0000121 +name: measurement datum + +[Term] +id: COB:0001000 +name: exposure of organism +def: "A process during which an organism comes into contact with another entity." [] +is_a: BFO:0000015 ! process + [Term] id: ENVO:01000254 name: environmental system @@ -183,10 +207,14 @@ is_a: ENVO:01000254 ! environmental system [Term] id: GO:0003674 +name: gene product or complex activity name: molecular_function def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +comment: This is the same as GO molecular function synonym: "molecular function" EXACT [] +is_a: BFO:0000015 ! process +disjoint_from: GO:0008150 ! biological_process [Term] id: GO:0004842 @@ -333,23 +361,30 @@ is_a: GO:0003674 ! molecular_function [Term] id: GO:0005634 +name: cell nucleus name: nucleus def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] synonym: "cell nucleus" EXACT [] synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757] xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus +is_a: BFO:0000040 ! material entity [Term] id: GO:0008150 +name: biological process name: biological_process def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." [] +comment: A biological process is an evolved process comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process +relationship: BFO:0000051 GO:0003674 ! has part molecular_function created_by: jl creation_date: 2012-09-19T15:05:24Z @@ -388,6 +423,40 @@ property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 "GROUP:OBI:" xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string +[Term] +id: OBI:0000047 +name: processed material +def: "Is a material entity that is created or changed during material processing." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000111 "processed material" xsd:string +property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string + +[Term] +id: OBI:0000967 +name: container +def: "A device that can be used to restrict the location of material entities over time" [] +is_a: OBI:0000968 ! device +property_value: IAO:0000111 "container" xsd:string +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string + +[Term] +id: OBI:0000968 +name: device +def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." [] +is_a: OBI:0000047 ! processed material +property_value: IAO:0000111 "device" xsd:string +property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string +property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." xsd:string +property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string +property_value: IAO:0000118 "instrument" xsd:string +property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string + [Term] id: OBI:0100026 name: organism @@ -414,7 +483,7 @@ is_a: BFO:0000016 ! disposition id: PATO:0000001 name: quality def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic [Term] id: PATO:0000402 @@ -441,14 +510,14 @@ creation_date: 2009-10-06T04:37:14Z [Term] id: RO:0002310 -name: exposure event or process -def: "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] -is_a: BFO:0000015 ! process +name: obsolete exposure event or process +def: "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/pull/173" xsd:anyURI +is_obsolete: true created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:55:39Z @@ -498,7 +567,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -524,7 +592,6 @@ synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 -xref: FBbt:00005099 xref: NLX:147821 is_a: UBERON:0000061 ! anatomical structure @@ -539,7 +606,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -563,7 +629,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -582,11 +647,11 @@ subset: common_anatomy subset: upper_level xref: AAO:0010841 xref: AEO:0000000 +xref: BFO:0000004 xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -601,6 +666,77 @@ is_a: BFO:0000004 ! independent continuant property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0001981 +name: blood vessel +def: "A vessel through which blood circulates in the body." [BTO:0001102, Wikipedia:Blood_vessel] +subset: efo_slim +subset: human_reference_atlas +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "region of vascular tree organ" EXACT [FMA:50722] +synonym: "vascular element" BROAD [EMAPA:35993] +synonym: "vascular tree organ region" EXACT [FMA:50722] +xref: AAO:0011004 +xref: AEO:0000207 +xref: BTO:0001102 +xref: CALOHA:TS-0080 +xref: EFO:0000817 +xref: EHDAA2:0003252 +xref: EHDAA:240 +xref: EMAPA:32743 +xref: EMAPA:35993 +xref: FMA:50722 +xref: FMA:63183 +xref: GAID:169 +xref: MA:0000060 +xref: MAT:0000393 +xref: MESH:D001808 +xref: NCIT:C12679 +xref: NLXANAT:090901 +xref: SCTID:361097006 +xref: TAO:0002137 +xref: UMLS:C0005847 {source="ncithesaurus:Blood_Vessel"} +xref: VHOG:0001250 +xref: Wikipedia:Blood_vessel +xref: XAO:0001011 +xref: ZFA:0005314 +is_a: UBERON:0010000 ! multicellular anatomical structure +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string + +[Term] +id: UBERON:0001982 +name: capillary +def: "Any of the smallest blood vessels connecting arterioles with venules." [https://github.com/obophenotype/uberon/issues/137, ISBN:0073040584, Wikipedia:Capillary] +subset: efo_slim +subset: human_reference_atlas +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "blood capillary" EXACT [] +synonym: "capillary vessel" EXACT [] +xref: AAO:0010252 +xref: BTO:0002045 +xref: CALOHA:TS-2006 +xref: EFO:0001906 +xref: EMAPA:35198 +xref: EV:0100035 +xref: FMA:63194 +xref: MA:0000065 +xref: MESH:D002196 +xref: NCIT:C12685 +xref: NLXANAT:090902 +xref: TAO:0005250 +xref: UMLS:C0935624 {source="ncithesaurus:Capillary"} +xref: VHOG:0001253 +xref: Wikipedia:Capillary +xref: XAO:0000116 +xref: ZFA:0005250 +is_a: UBERON:0001981 ! blood vessel +property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string + [Term] id: UBERON:0010000 name: multicellular anatomical structure @@ -609,7 +745,6 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 is_a: UBERON:0000061 ! anatomical structure property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:4751 @@ -753,6 +888,7 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process @@ -796,7 +932,8 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string +range: BFO:0000020 ! characteristic is_inverse_functional: true [Typedef] @@ -824,6 +961,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 @@ -834,7 +972,7 @@ def: "A relationship between a generically dependent continuant and a specifical property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000031 ! generically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! characteristic inverse_of: RO:0000059 ! concretizes [Typedef] @@ -843,7 +981,7 @@ name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string -domain: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic range: BFO:0000031 ! generically dependent continuant [Typedef] @@ -1065,8 +1203,8 @@ property_value: IAO:0000116 "Most location relations will only hold at certain t property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true transitive_over: BFO:0000050 ! part of @@ -1175,8 +1313,10 @@ is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 -name: regulates in other organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 ! process range: BFO:0000015 ! process @@ -1723,7 +1863,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -1903,7 +2043,7 @@ def: "a is attached to part of b if a is attached to b, or a is attached to some property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1969,6 +2109,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -2155,7 +2296,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -2195,7 +2336,7 @@ def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -2433,7 +2574,7 @@ id: RO:0002244 name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 ! exposure event or process +domain: COB:0001000 ! exposure of organism is_a: RO:0002410 ! causally related to [Typedef] @@ -2672,7 +2813,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 -name: results in formation of +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -2820,7 +2961,7 @@ property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -2937,7 +3078,7 @@ name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -3221,7 +3362,7 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3581,7 +3722,7 @@ is_a: RO:0002424 ! differs in id: RO:0002426 name: differs in attribute property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! characteristic is_a: RO:0002424 ! differs in [Typedef] @@ -3644,7 +3785,7 @@ property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd: property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -4078,7 +4219,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 @@ -4312,7 +4453,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system range: BFO:0000040 ! material entity -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -4563,7 +4704,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of is_asymmetric: true @@ -4754,8 +4895,8 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string -domain: BFO:0000020 ! specifically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic +range: BFO:0000020 ! characteristic [Typedef] id: RO:0002574 @@ -4823,7 +4964,7 @@ is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results in synthesis of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 @@ -4831,7 +4972,7 @@ name: results in assembly of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] @@ -5132,6 +5273,26 @@ property_value: IAO:0000119 Communal:roosting is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with +[Typedef] +id: RO:0002802 +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: RO:0002454 ! has host + [Typedef] id: RO:0003000 name: produces @@ -6066,6 +6227,28 @@ is_a: RO:0012011 ! indirectly causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z +[Typedef] +id: RO:0012013 +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + +[Typedef] +id: RO:0012014 +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: RO:0013001 name: has synaptic IO in region @@ -6322,6 +6505,16 @@ property_value: IAO:0000118 "inversely correlated with" xsd:string is_symmetric: true is_a: RO:0002610 ! correlated with +[Typedef] +id: RO:0017005 +name: contains measured amount +def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2999-0103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-5714-991X +property_value: IAO:0000112 "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." xsd:string +domain: OBI:0000967 ! container +range: COB:0000121 ! measurement datum + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -6441,7 +6634,7 @@ synonym: "is desmotrope of" EXACT [] xref: obo:chebi#is_tautomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38707", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38709"} +property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {seeAlso="CHEBI:38707", seeAlso="CHEBI:38709"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6453,7 +6646,7 @@ def: "Group A is a substituent group from Chemical B if A represents the functio xref: obo:chebi#is_substituent_group_from property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:30795", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:58957"} +property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {seeAlso="CHEBI:30795", seeAlso="CHEBI:58957"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6464,7 +6657,7 @@ def: "Chemical A has functional parent Chemical B if there is chemical transform xref: obo:chebi#has_functional_parent property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50851", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50854"} +property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {seeAlso="CHEBI:50851", seeAlso="CHEBI:50854"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6476,7 +6669,7 @@ synonym: "is optical isomer of" EXACT [] xref: obo:chebi#is_enantiomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:31472"} +property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", seeAlso="CHEBI:31472"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6488,7 +6681,7 @@ def: "Chemical A has parent hydride Chemical B if there exists a molecular graph xref: obo:chebi#has_parent_hydride property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:39106", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:52083"} +property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {seeAlso="CHEBI:39106", seeAlso="CHEBI:52083"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6526,6 +6719,40 @@ def: "Relates a gene to condition, such that a variation in this gene predispose is_a: RO:0003304 ! contributes to condition created_by: https://orcid.org/0000-0002-4142-7153 +[Typedef] +id: RO:0020101 +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 ! blood vessel +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002178 ! supplies + +[Typedef] +id: RO:0020102 +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 ! blood vessel +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002179 ! drains + +[Typedef] +id: RO:0020103 +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 ! capillary +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002178 ! supplies +is_a: RO:0002179 ! drains + [Typedef] id: RO:0040035 name: disease relationship diff --git a/ro-full.owl b/ro-full.owl index 6795b17f..8f426451 100644 --- a/ro-full.owl +++ b/ro-full.owl @@ -17,15 +17,14 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2023-08-18 + 2024-02-13 https://github.com/oborel/obo-relations/ @@ -42,12 +41,6 @@ - - - - - - @@ -1126,59 +1119,81 @@ Where we have an annotation assertion - + - + - + - + + + - + - + + + - + - + + + - + - + + + - + - + + + - + - + - + - + + + + + + + + + + + + + - + - + @@ -1476,23 +1491,6 @@ Where we have an annotation assertion - - - - - - - - - - - + @@ -4454,7 +4463,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to @@ -4821,7 +4830,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results in formation of + results in formation of anatomical entity @@ -5278,6 +5287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -8714,6 +8724,34 @@ the a supports either the existence of b, or the truth value of b. + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -10180,6 +10218,36 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + positively regulates in other organism + + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + negatively regulates in other organism + + negatively regulates in another organism + + + + @@ -10621,6 +10689,20 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. + A relation between a container and measurement datum that specifies the actual amount of material in the container. + + + contains measured amount + + + + @@ -10991,6 +11073,52 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + directly supplies and drains + + + + @@ -12777,6 +12905,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + @@ -12812,6 +12946,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable realizable entity @@ -12842,10 +12977,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + characteristic specifically dependent continuant + https://github.com/OBOFoundry/COB/issues/65 + https://github.com/oborel/obo-relations/pull/284 @@ -12931,6 +13075,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + A material entity that has a plasma membrane and results from cellular division. CALOHA:TS-2035 FBbt:00007002 FMA:68646 @@ -12940,8 +13085,11 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu VHOG:0001533 WBbt:0004017 XAO:0003012 + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell + cell @@ -12999,6 +13147,24 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + measurement datum + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + @@ -13043,10 +13209,14 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -13997,12 +14167,14 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus GO:0005634 + cell nucleus nucleus @@ -14026,7 +14198,15 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process @@ -14035,7 +14215,9 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu single organism process single-organism process GO:0008150 + A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + biological process biological_process @@ -14163,6 +14345,62 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + Is a material entity that is created or changed during material processing. + PERSON: Alan Ruttenberg + processed material + + + + + + + + + container + + A device that can be used to restrict the location of material entities over time + 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) + PERSON: Bjoern Peters + container + + + + + + + + + device + A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + +2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: + +(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. + +(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. + +(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. + +In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + PERSON: Helen Parkinson + instrument + OBI development call 2012-12-17. + device + + + + @@ -14271,16 +14509,16 @@ This issue is outside the scope of OBI. - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. + OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. 2017-06-05T17:55:39Z - exposure event or process + obsolete exposure event or process https://github.com/oborel/obo-relations/pull/173 + true @@ -14351,7 +14589,6 @@ This issue is outside the scope of OBI. CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -14393,7 +14630,6 @@ This issue is outside the scope of OBI. A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 - FBbt:00005099 NLX:147821 funiculus nerve fiber bundle @@ -14432,7 +14668,6 @@ This issue is outside the scope of OBI. BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -14465,7 +14700,6 @@ This issue is outside the scope of OBI. BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -14501,11 +14735,11 @@ This issue is outside the scope of OBI. AAO:0010841 AEO:0000000 + BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -14537,6 +14771,132 @@ This issue is outside the scope of OBI. + + + + + A vessel through which blood circulates in the body. + consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus + vascular element + AAO:0011004 + AEO:0000207 + BTO:0001102 + CALOHA:TS-0080 + EFO:0000817 + EHDAA2:0003252 + EHDAA:240 + EMAPA:32743 + EMAPA:35993 + FMA:50722 + FMA:63183 + GAID:169 + MA:0000060 + MAT:0000393 + MESH:D001808 + NCIT:C12679 + NLXANAT:090901 + SCTID:361097006 + TAO:0002137 + UMLS:C0005847 + VHOG:0001250 + Wikipedia:Blood_vessel + XAO:0001011 + ZFA:0005314 + region of vascular tree organ + vascular tree organ region + UBERON:0001981 + + + + + + blood vessel + + + + + A vessel through which blood circulates in the body. + BTO:0001102 + Wikipedia:Blood_vessel + + + + + vascular element + EMAPA:35993 + + + + + UMLS:C0005847 + ncithesaurus:Blood_Vessel + + + + + region of vascular tree organ + FMA:50722 + + + + + vascular tree organ region + FMA:50722 + + + + + + + + + Any of the smallest blood vessels connecting arterioles with venules. + not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element + AAO:0010252 + BTO:0002045 + CALOHA:TS-2006 + EFO:0001906 + EMAPA:35198 + EV:0100035 + FMA:63194 + MA:0000065 + MESH:D002196 + NCIT:C12685 + NLXANAT:090902 + TAO:0005250 + UMLS:C0935624 + VHOG:0001253 + Wikipedia:Capillary + XAO:0000116 + ZFA:0005250 + blood capillary + capillary vessel + UBERON:0001982 + + + + + + capillary + https://github.com/obophenotype/uberon/issues/2186 + + + + + Any of the smallest blood vessels connecting arterioles with venules. + ISBN:0073040584 + Wikipedia:Capillary + https://github.com/obophenotype/uberon/issues/137 + + + + + UMLS:C0935624 + ncithesaurus:Capillary + + + + @@ -14545,7 +14905,6 @@ This issue is outside the scope of OBI. CARO:0010000 - FBbt:00100313 multicellular structure UBERON:0010000 @@ -14751,6 +15110,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0001-6677-8489 + Aleix Puig-Barbé + + + + + Researcher ORCID=0000-0001-6677-8489 + + + + + + Aleix Puig-Barbé + + + + + @@ -14835,6 +15215,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-2999-0103) + Jie Zheng + + + + + researcher (ORCID 0000-0002-2999-0103) + + + + + + Jie Zheng + + + + + @@ -14856,6 +15257,27 @@ binary, and takes no temporal argument. + + + + researcher + Christian J Stoeckert + + + + + researcher + + + + + + Christian J Stoeckert + + + + + @@ -14982,6 +15404,48 @@ binary, and takes no temporal argument. + + + + Canadian biocurator + Pascale Gaudet + + + + + Canadian biocurator + + + + + + Pascale Gaudet + + + + + + + + + Researcher ORCID=0000-0003-1909-9269 + S. Clint Dowland + + + + + Researcher ORCID=0000-0003-1909-9269 + + + + + + S. Clint Dowland + + + + + @@ -15003,6 +15467,27 @@ binary, and takes no temporal argument. + + + + software/data engineer + Jorrit Poelen + + + + + software/data engineer + + + + + + Jorrit Poelen + + + + + @@ -15511,10 +15996,10 @@ No imports /////////////////////////////////////////////////////////////////////////////////////// --> - + - + @@ -15532,66 +16017,54 @@ No imports - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - @@ -15604,8 +16077,8 @@ No imports - - + + @@ -15615,7 +16088,7 @@ No imports - + @@ -15625,7 +16098,7 @@ No imports - + @@ -15642,8 +16115,8 @@ No imports - - + + @@ -15905,7 +16378,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -15915,8 +16388,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15926,8 +16399,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15944,8 +16417,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15964,7 +16437,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -15974,8 +16447,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15985,8 +16458,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16003,8 +16476,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16021,8 +16494,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16032,7 +16505,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16042,8 +16515,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16053,8 +16526,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16073,8 +16546,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16092,8 +16565,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16103,8 +16576,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16114,8 +16587,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16132,8 +16605,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16150,8 +16623,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16161,8 +16634,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16172,8 +16645,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16190,8 +16663,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16208,8 +16681,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16219,8 +16692,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16230,8 +16703,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16248,8 +16721,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16266,8 +16739,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16277,8 +16750,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16293,8 +16766,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16311,8 +16784,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16322,8 +16795,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16338,8 +16811,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16356,8 +16829,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16367,8 +16840,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16383,8 +16856,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16401,8 +16874,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16412,8 +16885,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16428,8 +16901,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16446,8 +16919,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16457,8 +16930,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16473,8 +16946,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16491,8 +16964,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16502,8 +16975,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16518,7 +16991,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16528,7 +17001,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16547,8 +17020,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16558,8 +17031,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16574,7 +17047,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16584,7 +17057,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16646,8 +17119,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16657,8 +17130,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16673,8 +17146,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16690,8 +17163,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16700,9 +17173,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16716,9 +17189,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16734,8 +17207,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16744,9 +17217,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16760,7 +17233,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16861,5 +17334,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/ro.json b/ro.json index e0aadc9d..447a2acb 100644 --- a/ro.json +++ b/ro.json @@ -13,12 +13,12 @@ "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -153,7 +153,14 @@ "definition" : { "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" }, - "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ] + "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/OBOFoundry/COB/issues/65" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", @@ -459,10 +466,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", - "xrefs" : [ "CARO:mah" ] + "val" : "A material entity that has a plasma membrane and results from cellular division." }, - "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], + "comments" : [ "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.", "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).", "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism." ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -536,6 +542,19 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/COB_0000121", + "lbl" : "measurement datum", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/COB_0001000", + "lbl" : "exposure of organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process during which an organism comes into contact with another entity." + } + } }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", "lbl" : "environmental system", @@ -596,7 +615,7 @@ "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", "xrefs" : [ "GOC:pdt" ] }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], + "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "This is the same as GO molecular function" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecular function" @@ -924,10 +943,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", - "xrefs" : [ "GOC:pdt" ] + "val" : "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." }, - "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological process" @@ -2273,6 +2291,84 @@ "val" : "EL++ ontology module" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000047", + "lbl" : "processed material", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Is a material entity that is created or changed during material processing." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "processed material" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000967", + "lbl" : "container", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A device that can be used to restrict the location of material entities over time" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "container" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000123" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000968", + "lbl" : "device", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "device" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A voltmeter is a measurement device which is intended to perform some measure function." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Helen Parkinson" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "instrument" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI development call 2012-12-17." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0100026", "lbl" : "organism", @@ -2625,6 +2721,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -3359,12 +3458,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -6139,7 +6243,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -6356,11 +6460,11 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002310", - "lbl" : "exposure event or process", + "lbl" : "obsolete exposure event or process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." + "val" : "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -6383,7 +6487,8 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" - } ] + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002312", @@ -11025,6 +11130,43 @@ "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", @@ -12697,6 +12839,54 @@ "val" : "2022-09-26T06:08:01Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -13181,6 +13371,25 @@ "val" : "https://orcid.org/0000-0003-1909-9269" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017005", + "lbl" : "contains measured amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2999-0103" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-5714-991X" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -13592,6 +13801,63 @@ "val" : "https://orcid.org/0000-0002-4142-7153" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -15527,8 +15793,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -15586,8 +15850,6 @@ } ], "xrefs" : [ { "val" : "CARO:0001001" - }, { - "val" : "FBbt:00005099" }, { "val" : "NLX:147821" } ] @@ -15612,8 +15874,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -15658,8 +15918,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -15693,6 +15951,8 @@ "val" : "AAO:0010841" }, { "val" : "AEO:0000000" + }, { + "val" : "BFO:0000004" }, { "val" : "BILA:0000000" }, { @@ -15701,8 +15961,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -15732,6 +15990,143 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "lbl" : "blood vessel", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vessel through which blood circulates in the body.", + "xrefs" : [ "BTO:0001102", "Wikipedia:Blood_vessel" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "vascular element", + "xrefs" : [ "EMAPA:35993" ] + }, { + "pred" : "hasExactSynonym", + "val" : "region of vascular tree organ", + "xrefs" : [ "FMA:50722" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vascular tree organ region", + "xrefs" : [ "FMA:50722" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011004" + }, { + "val" : "AEO:0000207" + }, { + "val" : "BTO:0001102" + }, { + "val" : "CALOHA:TS-0080" + }, { + "val" : "EFO:0000817" + }, { + "val" : "EHDAA2:0003252" + }, { + "val" : "EHDAA:240" + }, { + "val" : "EMAPA:32743" + }, { + "val" : "EMAPA:35993" + }, { + "val" : "FMA:50722" + }, { + "val" : "FMA:63183" + }, { + "val" : "GAID:169" + }, { + "val" : "MA:0000060" + }, { + "val" : "MAT:0000393" + }, { + "val" : "MESH:D001808" + }, { + "val" : "NCIT:C12679" + }, { + "val" : "NLXANAT:090901" + }, { + "val" : "SCTID:361097006" + }, { + "val" : "TAO:0002137" + }, { + "val" : "UMLS:C0005847" + }, { + "val" : "VHOG:0001250" + }, { + "val" : "Wikipedia:Blood_vessel" + }, { + "val" : "XAO:0001011" + }, { + "val" : "ZFA:0005314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001982", + "lbl" : "capillary", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any of the smallest blood vessels connecting arterioles with venules.", + "xrefs" : [ "ISBN:0073040584", "Wikipedia:Capillary", "https://github.com/obophenotype/uberon/issues/137" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blood capillary" + }, { + "pred" : "hasExactSynonym", + "val" : "capillary vessel" + } ], + "xrefs" : [ { + "val" : "AAO:0010252" + }, { + "val" : "BTO:0002045" + }, { + "val" : "CALOHA:TS-2006" + }, { + "val" : "EFO:0001906" + }, { + "val" : "EMAPA:35198" + }, { + "val" : "EV:0100035" + }, { + "val" : "FMA:63194" + }, { + "val" : "MA:0000065" + }, { + "val" : "MESH:D002196" + }, { + "val" : "NCIT:C12685" + }, { + "val" : "NLXANAT:090902" + }, { + "val" : "TAO:0005250" + }, { + "val" : "UMLS:C0935624" + }, { + "val" : "VHOG:0001253" + }, { + "val" : "Wikipedia:Capillary" + }, { + "val" : "XAO:0000116" + }, { + "val" : "ZFA:0005250" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2186" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", "lbl" : "multicellular anatomical structure", @@ -15749,8 +16144,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -15938,6 +16331,16 @@ "val" : "is defined by" } ] } + }, { + "id" : "https://orcid.org/0000-0001-6677-8489", + "lbl" : "Aleix Puig-Barbé", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0001-6677-8489" + } ] + } }, { "id" : "https://orcid.org/0000-0001-6996-0040", "lbl" : "Austin Meier", @@ -15978,6 +16381,16 @@ "val" : "data scientist" } ] } + }, { + "id" : "https://orcid.org/0000-0002-2999-0103", + "lbl" : "Jie Zheng", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-2999-0103)" + } ] + } }, { "id" : "https://orcid.org/0000-0002-4366-3088", "lbl" : "Pier Luigi Buttigieg", @@ -15988,6 +16401,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-5714-991X", + "lbl" : "Christian J Stoeckert", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-6601-2165", "lbl" : "Christopher J. Mungall", @@ -16048,6 +16471,26 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1813-6857", + "lbl" : "Pascale Gaudet", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Canadian biocurator" + } ] + } + }, { + "id" : "https://orcid.org/0000-0003-1909-9269", + "lbl" : "S. Clint Dowland", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-1909-9269" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1940-6740", "lbl" : "Anna Maria Masci", @@ -16058,6 +16501,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-3138-4118", + "lbl" : "Jorrit Poelen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "software/data engineer" + } ] + } }, { "id" : "https://orcid.org/0000-0003-4423-4370", "lbl" : "Charles Tapley Hoyt", @@ -16133,6 +16586,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000540", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/COB_0001000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", @@ -16141,10 +16598,26 @@ "sub" : "http://purl.obolibrary.org/obo/ENVO_01000739", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0003674", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0004842", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0003674" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0005634", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0008150", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0008150", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0003674" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0016301", "pred" : "is_a", @@ -16157,6 +16630,18 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000030", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000047", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000967", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000968" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000968", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000047" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0100026", "pred" : "is_a", @@ -16181,10 +16666,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002124", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002310", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002532", "pred" : "http://purl.obolibrary.org/obo/RO_0002524", @@ -16229,6 +16710,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010000" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001982", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010000", "pred" : "is_a", @@ -16633,6 +17122,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -18105,6 +18598,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -18517,6 +19018,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -18693,6 +19202,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -19369,6 +19894,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003000", "pred" : "inverseOf", @@ -19468,6 +19997,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -19507,6 +20040,13 @@ "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -19525,7 +20065,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", @@ -19533,7 +20073,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", @@ -19699,7 +20239,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -20011,10 +20551,26 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0017005", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000967" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000121" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/ro.obo b/ro.obo index 9cd84f7c..29ad9099 100644 --- a/ro.obo +++ b/ro.obo @@ -1,19 +1,24 @@ format-version: 1.2 -data-version: releases/2023-08-18 +data-version: releases/2024-02-13 subsetdef: common_anatomy "" +subsetdef: efo_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: human_reference_atlas "" +subsetdef: pheno_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" +subsetdef: uberon_slim "" subsetdef: upper_level "" +subsetdef: vertebrate_core "" ontology: ro property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Term] id: BFO:0000002 @@ -37,7 +42,7 @@ name: independent continuant def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000020 ! characteristic disjoint_from: BFO:0000031 ! generically dependent continuant relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant @@ -52,6 +57,7 @@ name: process def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000015 {all_only="true"} ! part of process relationship: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process [Term] @@ -62,26 +68,31 @@ disjoint_from: BFO:0000023 ! role [Term] id: BFO:0000017 +name: realizable name: realizable entity def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic disjoint_from: BFO:0000019 ! quality relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity [Term] id: BFO:0000019 name: quality -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 +name: characteristic name: specifically dependent continuant def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of characteristic +relationship: BFO:0000051 BFO:0000020 {all_only="true"} ! has part characteristic +property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string [Term] id: BFO:0000023 @@ -122,7 +133,10 @@ is_a: PATO:0000001 ! quality id: CL:0000000 name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] +def: "A material entity that has a plasma membrane and results from cellular division." [] +comment: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). +comment: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. xref: CALOHA:TS-2035 xref: FBbt:00007002 xref: FMA:68646 @@ -160,6 +174,16 @@ xref: WBbt:0003679 is_a: CL:0000000 ! cell property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: COB:0000121 +name: measurement datum + +[Term] +id: COB:0001000 +name: exposure of organism +def: "A process during which an organism comes into contact with another entity." [] +is_a: BFO:0000015 ! process + [Term] id: ENVO:01000254 name: environmental system @@ -183,10 +207,14 @@ is_a: ENVO:01000254 ! environmental system [Term] id: GO:0003674 +name: gene product or complex activity name: molecular_function def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +comment: This is the same as GO molecular function synonym: "molecular function" EXACT [] +is_a: BFO:0000015 ! process +disjoint_from: GO:0008150 ! biological_process [Term] id: GO:0004842 @@ -333,23 +361,30 @@ is_a: GO:0003674 ! molecular_function [Term] id: GO:0005634 +name: cell nucleus name: nucleus def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] synonym: "cell nucleus" EXACT [] synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757] xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus +is_a: BFO:0000040 ! material entity [Term] id: GO:0008150 +name: biological process name: biological_process def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." [] +comment: A biological process is an evolved process comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process +relationship: BFO:0000051 GO:0003674 ! has part molecular_function created_by: jl creation_date: 2012-09-19T15:05:24Z @@ -388,6 +423,40 @@ property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 "GROUP:OBI:" xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string +[Term] +id: OBI:0000047 +name: processed material +def: "Is a material entity that is created or changed during material processing." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000111 "processed material" xsd:string +property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string + +[Term] +id: OBI:0000967 +name: container +def: "A device that can be used to restrict the location of material entities over time" [] +is_a: OBI:0000968 ! device +property_value: IAO:0000111 "container" xsd:string +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string + +[Term] +id: OBI:0000968 +name: device +def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." [] +is_a: OBI:0000047 ! processed material +property_value: IAO:0000111 "device" xsd:string +property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string +property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." xsd:string +property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string +property_value: IAO:0000118 "instrument" xsd:string +property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string + [Term] id: OBI:0100026 name: organism @@ -414,7 +483,7 @@ is_a: BFO:0000016 ! disposition id: PATO:0000001 name: quality def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic [Term] id: PATO:0000402 @@ -441,14 +510,14 @@ creation_date: 2009-10-06T04:37:14Z [Term] id: RO:0002310 -name: exposure event or process -def: "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] -is_a: BFO:0000015 ! process +name: obsolete exposure event or process +def: "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/pull/173" xsd:anyURI +is_obsolete: true created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:55:39Z @@ -498,7 +567,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -524,7 +592,6 @@ synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 -xref: FBbt:00005099 xref: NLX:147821 is_a: UBERON:0000061 ! anatomical structure @@ -539,7 +606,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -563,7 +629,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -582,11 +647,11 @@ subset: common_anatomy subset: upper_level xref: AAO:0010841 xref: AEO:0000000 +xref: BFO:0000004 xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -601,6 +666,77 @@ is_a: BFO:0000004 ! independent continuant property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0001981 +name: blood vessel +def: "A vessel through which blood circulates in the body." [BTO:0001102, Wikipedia:Blood_vessel] +subset: efo_slim +subset: human_reference_atlas +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "region of vascular tree organ" EXACT [FMA:50722] +synonym: "vascular element" BROAD [EMAPA:35993] +synonym: "vascular tree organ region" EXACT [FMA:50722] +xref: AAO:0011004 +xref: AEO:0000207 +xref: BTO:0001102 +xref: CALOHA:TS-0080 +xref: EFO:0000817 +xref: EHDAA2:0003252 +xref: EHDAA:240 +xref: EMAPA:32743 +xref: EMAPA:35993 +xref: FMA:50722 +xref: FMA:63183 +xref: GAID:169 +xref: MA:0000060 +xref: MAT:0000393 +xref: MESH:D001808 +xref: NCIT:C12679 +xref: NLXANAT:090901 +xref: SCTID:361097006 +xref: TAO:0002137 +xref: UMLS:C0005847 {source="ncithesaurus:Blood_Vessel"} +xref: VHOG:0001250 +xref: Wikipedia:Blood_vessel +xref: XAO:0001011 +xref: ZFA:0005314 +is_a: UBERON:0010000 ! multicellular anatomical structure +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string + +[Term] +id: UBERON:0001982 +name: capillary +def: "Any of the smallest blood vessels connecting arterioles with venules." [https://github.com/obophenotype/uberon/issues/137, ISBN:0073040584, Wikipedia:Capillary] +subset: efo_slim +subset: human_reference_atlas +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "blood capillary" EXACT [] +synonym: "capillary vessel" EXACT [] +xref: AAO:0010252 +xref: BTO:0002045 +xref: CALOHA:TS-2006 +xref: EFO:0001906 +xref: EMAPA:35198 +xref: EV:0100035 +xref: FMA:63194 +xref: MA:0000065 +xref: MESH:D002196 +xref: NCIT:C12685 +xref: NLXANAT:090902 +xref: TAO:0005250 +xref: UMLS:C0935624 {source="ncithesaurus:Capillary"} +xref: VHOG:0001253 +xref: Wikipedia:Capillary +xref: XAO:0000116 +xref: ZFA:0005250 +is_a: UBERON:0001981 ! blood vessel +property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string + [Term] id: UBERON:0010000 name: multicellular anatomical structure @@ -609,7 +745,6 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 is_a: UBERON:0000061 ! anatomical structure property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:4751 @@ -753,6 +888,7 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process @@ -796,7 +932,8 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string +range: BFO:0000020 ! characteristic is_inverse_functional: true [Typedef] @@ -824,6 +961,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 @@ -834,7 +972,7 @@ def: "A relationship between a generically dependent continuant and a specifical property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000031 ! generically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! characteristic inverse_of: RO:0000059 ! concretizes [Typedef] @@ -843,7 +981,7 @@ name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string -domain: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic range: BFO:0000031 ! generically dependent continuant [Typedef] @@ -1065,8 +1203,8 @@ property_value: IAO:0000116 "Most location relations will only hold at certain t property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true transitive_over: BFO:0000050 ! part of @@ -1175,8 +1313,10 @@ is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 -name: regulates in other organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 ! process range: BFO:0000015 ! process @@ -1723,7 +1863,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -1903,7 +2043,7 @@ def: "a is attached to part of b if a is attached to b, or a is attached to some property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1969,6 +2109,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -2155,7 +2296,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -2195,7 +2336,7 @@ def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -2433,7 +2574,7 @@ id: RO:0002244 name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 ! exposure event or process +domain: COB:0001000 ! exposure of organism is_a: RO:0002410 ! causally related to [Typedef] @@ -2672,7 +2813,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 -name: results in formation of +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -2820,7 +2961,7 @@ property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -2937,7 +3078,7 @@ name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -3221,7 +3362,7 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3581,7 +3722,7 @@ is_a: RO:0002424 ! differs in id: RO:0002426 name: differs in attribute property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! characteristic is_a: RO:0002424 ! differs in [Typedef] @@ -3644,7 +3785,7 @@ property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd: property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -4078,7 +4219,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 @@ -4312,7 +4453,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system range: BFO:0000040 ! material entity -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -4563,7 +4704,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of is_asymmetric: true @@ -4754,8 +4895,8 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string -domain: BFO:0000020 ! specifically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic +range: BFO:0000020 ! characteristic [Typedef] id: RO:0002574 @@ -4823,7 +4964,7 @@ is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results in synthesis of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 @@ -4831,7 +4972,7 @@ name: results in assembly of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] @@ -5132,6 +5273,26 @@ property_value: IAO:0000119 Communal:roosting is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with +[Typedef] +id: RO:0002802 +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: RO:0002454 ! has host + [Typedef] id: RO:0003000 name: produces @@ -6066,6 +6227,28 @@ is_a: RO:0012011 ! indirectly causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z +[Typedef] +id: RO:0012013 +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + +[Typedef] +id: RO:0012014 +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: RO:0013001 name: has synaptic IO in region @@ -6322,6 +6505,16 @@ property_value: IAO:0000118 "inversely correlated with" xsd:string is_symmetric: true is_a: RO:0002610 ! correlated with +[Typedef] +id: RO:0017005 +name: contains measured amount +def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2999-0103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-5714-991X +property_value: IAO:0000112 "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." xsd:string +domain: OBI:0000967 ! container +range: COB:0000121 ! measurement datum + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -6441,7 +6634,7 @@ synonym: "is desmotrope of" EXACT [] xref: obo:chebi#is_tautomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38707", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38709"} +property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {seeAlso="CHEBI:38707", seeAlso="CHEBI:38709"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6453,7 +6646,7 @@ def: "Group A is a substituent group from Chemical B if A represents the functio xref: obo:chebi#is_substituent_group_from property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:30795", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:58957"} +property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {seeAlso="CHEBI:30795", seeAlso="CHEBI:58957"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6464,7 +6657,7 @@ def: "Chemical A has functional parent Chemical B if there is chemical transform xref: obo:chebi#has_functional_parent property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50851", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50854"} +property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {seeAlso="CHEBI:50851", seeAlso="CHEBI:50854"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6476,7 +6669,7 @@ synonym: "is optical isomer of" EXACT [] xref: obo:chebi#is_enantiomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:31472"} +property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", seeAlso="CHEBI:31472"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6488,7 +6681,7 @@ def: "Chemical A has parent hydride Chemical B if there exists a molecular graph xref: obo:chebi#has_parent_hydride property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:39106", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:52083"} +property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {seeAlso="CHEBI:39106", seeAlso="CHEBI:52083"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6526,6 +6719,40 @@ def: "Relates a gene to condition, such that a variation in this gene predispose is_a: RO:0003304 ! contributes to condition created_by: https://orcid.org/0000-0002-4142-7153 +[Typedef] +id: RO:0020101 +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 ! blood vessel +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002178 ! supplies + +[Typedef] +id: RO:0020102 +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 ! blood vessel +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002179 ! drains + +[Typedef] +id: RO:0020103 +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 ! capillary +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002178 ! supplies +is_a: RO:0002179 ! drains + [Typedef] id: RO:0040035 name: disease relationship diff --git a/ro.owl b/ro.owl index c50e7d26..8f5e4eb0 100644 --- a/ro.owl +++ b/ro.owl @@ -17,15 +17,14 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2023-08-18 + 2024-02-13 https://github.com/oborel/obo-relations/ @@ -42,12 +41,6 @@ - - - - - - @@ -1126,59 +1119,81 @@ Where we have an annotation assertion - + - + - + - + + + - + - + + + - + - + + + - + - + + + - + - + + + - + - + - + - + + + + + + + + + + + + + - + - + @@ -1476,23 +1491,6 @@ Where we have an annotation assertion - - - - - - - - - - - + @@ -4454,7 +4463,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to @@ -4821,7 +4830,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results in formation of + results in formation of anatomical entity @@ -5278,6 +5287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -8714,6 +8724,34 @@ the a supports either the existence of b, or the truth value of b. + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -10180,6 +10218,36 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + positively regulates in other organism + + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + negatively regulates in other organism + + negatively regulates in another organism + + + + @@ -10621,6 +10689,20 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. + A relation between a container and measurement datum that specifies the actual amount of material in the container. + + + contains measured amount + + + + @@ -10991,6 +11073,52 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + directly supplies and drains + + + + @@ -12777,6 +12905,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + @@ -12812,6 +12946,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable realizable entity @@ -12842,10 +12977,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + characteristic specifically dependent continuant + https://github.com/OBOFoundry/COB/issues/65 + https://github.com/oborel/obo-relations/pull/284 @@ -12931,6 +13075,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + A material entity that has a plasma membrane and results from cellular division. CALOHA:TS-2035 FBbt:00007002 FMA:68646 @@ -12940,8 +13085,11 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu VHOG:0001533 WBbt:0004017 XAO:0003012 + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell + cell @@ -12999,6 +13147,24 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + measurement datum + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + @@ -13043,10 +13209,14 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -13997,12 +14167,14 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus GO:0005634 + cell nucleus nucleus @@ -14026,7 +14198,15 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process @@ -14035,7 +14215,9 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu single organism process single-organism process GO:0008150 + A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + biological process biological_process @@ -14163,6 +14345,62 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + Is a material entity that is created or changed during material processing. + PERSON: Alan Ruttenberg + processed material + + + + + + + + + container + + A device that can be used to restrict the location of material entities over time + 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) + PERSON: Bjoern Peters + container + + + + + + + + + device + A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + +2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: + +(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. + +(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. + +(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. + +In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + PERSON: Helen Parkinson + instrument + OBI development call 2012-12-17. + device + + + + @@ -14271,16 +14509,16 @@ This issue is outside the scope of OBI. - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. + OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. 2017-06-05T17:55:39Z - exposure event or process + obsolete exposure event or process https://github.com/oborel/obo-relations/pull/173 + true @@ -14351,7 +14589,6 @@ This issue is outside the scope of OBI. CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -14393,7 +14630,6 @@ This issue is outside the scope of OBI. A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 - FBbt:00005099 NLX:147821 funiculus nerve fiber bundle @@ -14432,7 +14668,6 @@ This issue is outside the scope of OBI. BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -14465,7 +14700,6 @@ This issue is outside the scope of OBI. BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -14501,11 +14735,11 @@ This issue is outside the scope of OBI. AAO:0010841 AEO:0000000 + BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -14537,6 +14771,132 @@ This issue is outside the scope of OBI. + + + + + A vessel through which blood circulates in the body. + consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus + vascular element + AAO:0011004 + AEO:0000207 + BTO:0001102 + CALOHA:TS-0080 + EFO:0000817 + EHDAA2:0003252 + EHDAA:240 + EMAPA:32743 + EMAPA:35993 + FMA:50722 + FMA:63183 + GAID:169 + MA:0000060 + MAT:0000393 + MESH:D001808 + NCIT:C12679 + NLXANAT:090901 + SCTID:361097006 + TAO:0002137 + UMLS:C0005847 + VHOG:0001250 + Wikipedia:Blood_vessel + XAO:0001011 + ZFA:0005314 + region of vascular tree organ + vascular tree organ region + UBERON:0001981 + + + + + + blood vessel + + + + + A vessel through which blood circulates in the body. + BTO:0001102 + Wikipedia:Blood_vessel + + + + + vascular element + EMAPA:35993 + + + + + UMLS:C0005847 + ncithesaurus:Blood_Vessel + + + + + region of vascular tree organ + FMA:50722 + + + + + vascular tree organ region + FMA:50722 + + + + + + + + + Any of the smallest blood vessels connecting arterioles with venules. + not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element + AAO:0010252 + BTO:0002045 + CALOHA:TS-2006 + EFO:0001906 + EMAPA:35198 + EV:0100035 + FMA:63194 + MA:0000065 + MESH:D002196 + NCIT:C12685 + NLXANAT:090902 + TAO:0005250 + UMLS:C0935624 + VHOG:0001253 + Wikipedia:Capillary + XAO:0000116 + ZFA:0005250 + blood capillary + capillary vessel + UBERON:0001982 + + + + + + capillary + https://github.com/obophenotype/uberon/issues/2186 + + + + + Any of the smallest blood vessels connecting arterioles with venules. + ISBN:0073040584 + Wikipedia:Capillary + https://github.com/obophenotype/uberon/issues/137 + + + + + UMLS:C0935624 + ncithesaurus:Capillary + + + + @@ -14545,7 +14905,6 @@ This issue is outside the scope of OBI. CARO:0010000 - FBbt:00100313 multicellular structure UBERON:0010000 @@ -14751,6 +15110,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0001-6677-8489 + Aleix Puig-Barbé + + + + + Researcher ORCID=0000-0001-6677-8489 + + + + + + Aleix Puig-Barbé + + + + + @@ -14835,6 +15215,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-2999-0103) + Jie Zheng + + + + + researcher (ORCID 0000-0002-2999-0103) + + + + + + Jie Zheng + + + + + @@ -14856,6 +15257,27 @@ binary, and takes no temporal argument. + + + + researcher + Christian J Stoeckert + + + + + researcher + + + + + + Christian J Stoeckert + + + + + @@ -14982,6 +15404,48 @@ binary, and takes no temporal argument. + + + + Canadian biocurator + Pascale Gaudet + + + + + Canadian biocurator + + + + + + Pascale Gaudet + + + + + + + + + Researcher ORCID=0000-0003-1909-9269 + S. Clint Dowland + + + + + Researcher ORCID=0000-0003-1909-9269 + + + + + + S. Clint Dowland + + + + + @@ -15003,6 +15467,27 @@ binary, and takes no temporal argument. + + + + software/data engineer + Jorrit Poelen + + + + + software/data engineer + + + + + + Jorrit Poelen + + + + + @@ -15514,10 +15999,10 @@ No imports /////////////////////////////////////////////////////////////////////////////////////// --> - + - + @@ -15535,66 +16020,54 @@ No imports - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - @@ -15607,8 +16080,8 @@ No imports - - + + @@ -15618,7 +16091,7 @@ No imports - + @@ -15628,7 +16101,7 @@ No imports - + @@ -15645,8 +16118,8 @@ No imports - - + + @@ -15908,7 +16381,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -15918,8 +16391,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15929,8 +16402,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15947,8 +16420,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15967,7 +16440,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -15977,8 +16450,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15988,8 +16461,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16006,8 +16479,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16023,8 +16496,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16034,7 +16507,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16044,8 +16517,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16055,8 +16528,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16075,8 +16548,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16094,8 +16567,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16105,8 +16578,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16116,8 +16589,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16134,8 +16607,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16152,8 +16625,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16163,8 +16636,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16174,8 +16647,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16192,8 +16665,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16210,8 +16683,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16221,8 +16694,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16232,8 +16705,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16250,8 +16723,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16268,8 +16741,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16279,8 +16752,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16295,8 +16768,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16313,8 +16786,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16324,8 +16797,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16340,8 +16813,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16358,8 +16831,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16369,8 +16842,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16385,8 +16858,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16403,8 +16876,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16414,8 +16887,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16430,8 +16903,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16448,8 +16921,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16459,8 +16932,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16475,8 +16948,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16493,8 +16966,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16504,8 +16977,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16520,7 +16993,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16530,7 +17003,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16549,8 +17022,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16560,8 +17033,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16576,7 +17049,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16586,7 +17059,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16648,8 +17121,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16659,8 +17132,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16675,8 +17148,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16692,8 +17165,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16702,9 +17175,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16718,9 +17191,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16736,8 +17209,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16746,9 +17219,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16762,7 +17235,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16863,5 +17336,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/src/ontology/imports/orcidio_import.owl b/src/ontology/imports/orcidio_import.owl index 46124dcd..1044bba3 100644 --- a/src/ontology/imports/orcidio_import.owl +++ b/src/ontology/imports/orcidio_import.owl @@ -7,21 +7,27 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-08-16") + +Annotation(owl:versionInfo "2024-02-12") +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -34,6 +40,11 @@ Declaration(AnnotationProperty()) # Named Individuals ############################ +# Individual: (Aleix Puig-Barbé) + +AnnotationAssertion(Annotation( ) "Researcher ORCID=0000-0001-6677-8489") +AnnotationAssertion(Annotation( ) rdfs:label "Aleix Puig-Barbé") + # Individual: (Austin Meier) AnnotationAssertion(Annotation( ) "Researcher") @@ -54,11 +65,21 @@ AnnotationAssertion(Annotation( ) "data scientist") AnnotationAssertion(Annotation( ) rdfs:label "Anne Thessen") +# Individual: (Jie Zheng) + +AnnotationAssertion(Annotation( ) "researcher (ORCID 0000-0002-2999-0103)") +AnnotationAssertion(Annotation( ) rdfs:label "Jie Zheng") + # Individual: (Pier Luigi Buttigieg) AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Pier Luigi Buttigieg") +# Individual: (Christian J Stoeckert) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "Christian J Stoeckert") + # Individual: (Christopher J. Mungall) AnnotationAssertion(Annotation( ) "bioinformatics researcher") @@ -89,11 +110,26 @@ AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Lindsay G Cowell") +# Individual: (Pascale Gaudet) + +AnnotationAssertion(Annotation( ) "Canadian biocurator") +AnnotationAssertion(Annotation( ) rdfs:label "Pascale Gaudet") + +# Individual: (S. Clint Dowland) + +AnnotationAssertion(Annotation( ) "Researcher ORCID=0000-0003-1909-9269") +AnnotationAssertion(Annotation( ) rdfs:label "S. Clint Dowland") + # Individual: (Anna Maria Masci) AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Anna Maria Masci") +# Individual: (Jorrit Poelen) + +AnnotationAssertion(Annotation( ) "software/data engineer") +AnnotationAssertion(Annotation( ) rdfs:label "Jorrit Poelen") + # Individual: (Charles Tapley Hoyt) AnnotationAssertion(Annotation( ) "American chemist") diff --git a/src/ontology/subsets/ro-biotic-interaction.json b/src/ontology/subsets/ro-biotic-interaction.json index 8309ba7d..9fd62d8e 100644 --- a/src/ontology/subsets/ro-biotic-interaction.json +++ b/src/ontology/subsets/ro-biotic-interaction.json @@ -736,6 +736,43 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008501", "lbl" : "epiphyte of", @@ -1021,6 +1058,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002641", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002635" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "subPropertyOf", @@ -1113,6 +1158,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "inverseOf", diff --git a/src/ontology/subsets/ro-biotic-interaction.obo b/src/ontology/subsets/ro-biotic-interaction.obo index 1f33ac3f..82eed56a 100644 --- a/src/ontology/subsets/ro-biotic-interaction.obo +++ b/src/ontology/subsets/ro-biotic-interaction.obo @@ -441,6 +441,26 @@ def: "inverse of intracellular endoparasite of" [] subset: RO:0002259 is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002802 +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: RO:0002454 ! has host + [Typedef] id: RO:0008501 name: epiphyte of diff --git a/src/ontology/subsets/ro-biotic-interaction.owl b/src/ontology/subsets/ro-biotic-interaction.owl index 9017b92f..2373adf8 100644 --- a/src/ontology/subsets/ro-biotic-interaction.owl +++ b/src/ontology/subsets/ro-biotic-interaction.owl @@ -7,6 +7,7 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> @@ -65,6 +66,12 @@ + + + + + + @@ -754,6 +761,34 @@ + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -822,5 +857,5 @@ - + diff --git a/src/ontology/subsets/ro-causal.json b/src/ontology/subsets/ro-causal.json index 22c6414d..995c9dab 100644 --- a/src/ontology/subsets/ro-causal.json +++ b/src/ontology/subsets/ro-causal.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index aae8993f..b2bf3775 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index 40bb5909..5284eca2 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-causal.tsv b/src/ontology/subsets/ro-causal.tsv index f63b8b06..958994a5 100644 --- a/src/ontology/subsets/ro-causal.tsv +++ b/src/ontology/subsets/ro-causal.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid1 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid18 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid22 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid26 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid33 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid37 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid40 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid5 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid52 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid58 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid61 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid64 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid67 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid1 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid18 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid22 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid26 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid33 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid37 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid40 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid5 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid52 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid58 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid61 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid64 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid67 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid9 @@ -29,6 +29,7 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 + @@ -39,7 +40,6 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 - @@ -47,6 +47,8 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 + + diff --git a/src/ontology/subsets/ro-chado.json b/src/ontology/subsets/ro-chado.json index a473678c..492b6f02 100644 --- a/src/ontology/subsets/ro-chado.json +++ b/src/ontology/subsets/ro-chado.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/subsets/ro-chado.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/subsets/ro-chado.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -1838,6 +1838,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -2572,12 +2575,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -5352,7 +5360,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -10143,6 +10151,43 @@ "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", @@ -11815,6 +11860,54 @@ "val" : "2022-09-26T06:08:01Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -12299,6 +12392,25 @@ "val" : "https://orcid.org/0000-0003-1909-9269" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017005", + "lbl" : "contains measured amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2999-0103" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-5714-991X" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -12710,6 +12822,63 @@ "val" : "https://orcid.org/0000-0002-4142-7153" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -14789,6 +14958,16 @@ "val" : "is defined by" } ] } + }, { + "id" : "https://orcid.org/0000-0001-6677-8489", + "lbl" : "Aleix Puig-Barbé", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0001-6677-8489" + } ] + } }, { "id" : "https://orcid.org/0000-0001-6996-0040", "lbl" : "Austin Meier", @@ -14829,6 +15008,16 @@ "val" : "data scientist" } ] } + }, { + "id" : "https://orcid.org/0000-0002-2999-0103", + "lbl" : "Jie Zheng", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-2999-0103)" + } ] + } }, { "id" : "https://orcid.org/0000-0002-4366-3088", "lbl" : "Pier Luigi Buttigieg", @@ -14839,6 +15028,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-5714-991X", + "lbl" : "Christian J Stoeckert", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-6601-2165", "lbl" : "Christopher J. Mungall", @@ -14899,6 +15098,26 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1813-6857", + "lbl" : "Pascale Gaudet", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Canadian biocurator" + } ] + } + }, { + "id" : "https://orcid.org/0000-0003-1909-9269", + "lbl" : "S. Clint Dowland", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-1909-9269" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1940-6740", "lbl" : "Anna Maria Masci", @@ -14909,6 +15128,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-3138-4118", + "lbl" : "Jorrit Poelen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "software/data engineer" + } ] + } }, { "id" : "https://orcid.org/0000-0003-4423-4370", "lbl" : "Charles Tapley Hoyt", @@ -15308,6 +15537,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -16780,6 +17013,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -17192,6 +17433,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -17360,6 +17609,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -18036,6 +18301,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003000", "pred" : "inverseOf", diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index fe43ab79..dd45dd89 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -1,19 +1,24 @@ format-version: 1.2 subsetdef: common_anatomy "" +subsetdef: efo_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: human_reference_atlas "" +subsetdef: pheno_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" +subsetdef: uberon_slim "" subsetdef: upper_level "" +subsetdef: vertebrate_core "" default-namespace: relationship ontology: ro/subsets/ro-chado.obo property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Typedef] id: BFO:0000050 @@ -312,8 +317,9 @@ is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 -name: regulates_in_other_organism +name: regulates_in_another_organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "regulates in other organism" EXACT [] is_a: RO:0002418 ! causally upstream of or within [Typedef] @@ -630,7 +636,7 @@ id: RO:0002131 name: overlaps def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -735,7 +741,7 @@ is_a: RO:0002323 ! mereotopologically related to id: RO:0002177 name: attached_to_part_of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -775,6 +781,7 @@ id: RO:0002202 name: develops_from def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -883,7 +890,7 @@ is_a: RO:0002216 ! capable of part of id: RO:0002216 name: capable_of_part_of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -1229,7 +1236,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 -name: results_in_formation_of +name: results_in_formation_of_anatomical_entity is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -1307,7 +1314,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002314 name: characteristic_of_part_of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -1373,7 +1380,7 @@ def: "A grouping relationship for any relationship directly involving a function id: RO:0002329 name: part_of_structure_that_is_capable_of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -1843,7 +1850,7 @@ id: RO:0002432 name: is_active_in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -2114,7 +2121,7 @@ is_a: RO:0002476 ! child nucleus of id: RO:0002479 name: has_part_that_occurs_in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 @@ -2280,7 +2287,7 @@ is_a: RO:0002566 ! causally influences id: RO:0002509 name: determined_by_part_of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -2618,12 +2625,12 @@ is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results_in_synthesis_of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 name: results_in_assembly_of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] @@ -2871,6 +2878,19 @@ def: "Two or more individuals sharing the same roost site (cave, mine, tree or t is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with +[Typedef] +id: RO:0002802 +name: reservoir_host_of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has_reservoir_host +def: "inverse of reservoir host of" [] +is_a: RO:0002454 ! has host + [Typedef] id: RO:0003000 name: produces @@ -3498,6 +3518,20 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of +[Typedef] +id: RO:0012013 +name: positively_regulates_in_another_organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "positively regulates in other organism" EXACT [] +is_a: RO:0002010 ! regulates in another organism + +[Typedef] +id: RO:0012014 +name: negatively_regulates_in_another_organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "negatively regulates in other organism" EXACT [] +is_a: RO:0002010 ! regulates in another organism + [Typedef] id: RO:0013001 name: has_synaptic_IO_in_region @@ -3681,6 +3715,11 @@ def: "A relation between entities in which one increases as the other decreases. is_symmetric: true is_a: RO:0002610 ! correlated with +[Typedef] +id: RO:0017005 +name: contains_measured_amount +def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] + [Typedef] id: RO:0018001 name: is_myristoyltransferase_activity @@ -3820,6 +3859,25 @@ name: confers_susceptibility_to_condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] is_a: RO:0003304 ! contributes to condition +[Typedef] +id: RO:0020101 +name: vessel_supplies_blood_to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +is_a: RO:0002178 ! supplies + +[Typedef] +id: RO:0020102 +name: vessel_drains_blood_from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +is_a: RO:0002179 ! drains + +[Typedef] +id: RO:0020103 +name: directly_supplies_and_drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +is_a: RO:0002178 ! supplies +is_a: RO:0002179 ! drains + [Typedef] id: RO:0040035 name: disease_relationship diff --git a/src/ontology/subsets/ro-chado.owl b/src/ontology/subsets/ro-chado.owl index 389234a4..76b4fd58 100644 --- a/src/ontology/subsets/ro-chado.owl +++ b/src/ontology/subsets/ro-chado.owl @@ -17,12 +17,11 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2023-08-18 + + 2024-02-13 @@ -38,12 +37,6 @@ - - - - - - @@ -1122,59 +1115,81 @@ Where we have an annotation assertion - + - + - + - + + + - + - + + + - + - + + + - + - + + + - + - + + + - + - + - + - + + + + + + + + + + + + + - + - + @@ -1472,23 +1487,6 @@ Where we have an annotation assertion - - - - - - - - - - - + @@ -4538,7 +4545,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results in formation of + results in formation of anatomical entity @@ -4985,6 +4992,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -8278,6 +8286,34 @@ the a supports either the existence of b, or the truth value of b. + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -9636,6 +9672,36 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + positively regulates in other organism + + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + negatively regulates in other organism + + negatively regulates in another organism + + + + @@ -10065,6 +10131,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. + A relation between a container and measurement datum that specifies the actual amount of material in the container. + + + contains measured amount + + + + @@ -10433,6 +10511,46 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + vessel supplies blood to + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + vessel drains blood from + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + directly supplies and drains + + + + @@ -12276,6 +12394,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0001-6677-8489 + Aleix Puig-Barbé + + + + + Researcher ORCID=0000-0001-6677-8489 + + + + + + Aleix Puig-Barbé + + + + + @@ -12360,6 +12499,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-2999-0103) + Jie Zheng + + + + + researcher (ORCID 0000-0002-2999-0103) + + + + + + Jie Zheng + + + + + @@ -12381,6 +12541,27 @@ binary, and takes no temporal argument. + + + + researcher + Christian J Stoeckert + + + + + researcher + + + + + + Christian J Stoeckert + + + + + @@ -12507,6 +12688,48 @@ binary, and takes no temporal argument. + + + + Canadian biocurator + Pascale Gaudet + + + + + Canadian biocurator + + + + + + Pascale Gaudet + + + + + + + + + Researcher ORCID=0000-0003-1909-9269 + S. Clint Dowland + + + + + Researcher ORCID=0000-0003-1909-9269 + + + + + + S. Clint Dowland + + + + + @@ -12528,6 +12751,27 @@ binary, and takes no temporal argument. + + + + software/data engineer + Jorrit Poelen + + + + + software/data engineer + + + + + + Jorrit Poelen + + + + + @@ -13003,28 +13247,28 @@ No imports /////////////////////////////////////////////////////////////////////////////////////// --> - + - + - + - + - + - + - + - + @@ -13033,15 +13277,6 @@ No imports - - - - - - - - - @@ -13065,8 +13300,8 @@ No imports - - + + @@ -13076,8 +13311,8 @@ No imports - - + + @@ -13087,8 +13322,8 @@ No imports - - + + @@ -13105,8 +13340,8 @@ No imports - - + + @@ -13123,8 +13358,8 @@ No imports - - + + @@ -13134,8 +13369,8 @@ No imports - - + + @@ -13145,8 +13380,8 @@ No imports - - + + @@ -13163,8 +13398,8 @@ No imports - - + + @@ -13181,8 +13416,8 @@ No imports - - + + @@ -13192,8 +13427,8 @@ No imports - - + + @@ -13203,8 +13438,8 @@ No imports - - + + @@ -13221,8 +13456,8 @@ No imports - - + + @@ -13239,8 +13474,8 @@ No imports - - + + @@ -13250,8 +13485,8 @@ No imports - - + + @@ -13266,8 +13501,8 @@ No imports - - + + @@ -13284,8 +13519,8 @@ No imports - - + + @@ -13295,8 +13530,8 @@ No imports - - + + @@ -13311,8 +13546,8 @@ No imports - - + + @@ -13329,8 +13564,8 @@ No imports - - + + @@ -13340,8 +13575,8 @@ No imports - - + + @@ -13356,8 +13591,8 @@ No imports - - + + @@ -13374,8 +13609,8 @@ No imports - - + + @@ -13385,8 +13620,8 @@ No imports - - + + @@ -13401,8 +13636,8 @@ No imports - - + + @@ -13419,8 +13654,8 @@ No imports - - + + @@ -13430,8 +13665,8 @@ No imports - - + + @@ -13446,8 +13681,8 @@ No imports - - + + @@ -13507,8 +13742,8 @@ No imports - - + + @@ -13518,8 +13753,8 @@ No imports - - + + @@ -13534,8 +13769,8 @@ No imports - - + + @@ -13551,8 +13786,8 @@ No imports - - + + @@ -13561,9 +13796,9 @@ No imports - - - + + + @@ -13577,9 +13812,9 @@ No imports - - - + + + @@ -13595,8 +13830,8 @@ No imports - - + + @@ -13605,9 +13840,9 @@ No imports - - - + + + @@ -13621,7 +13856,7 @@ No imports - + @@ -13722,5 +13957,5 @@ No imports - + diff --git a/src/ontology/subsets/ro-developmental.json b/src/ontology/subsets/ro-developmental.json index f4109945..d6d32493 100644 --- a/src/ontology/subsets/ro-developmental.json +++ b/src/ontology/subsets/ro-developmental.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index 1b9a7611..6518ba78 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index d5a7ed64..5f2ee16a 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-developmental.tsv b/src/ontology/subsets/ro-developmental.tsv index 2409aaef..3095b994 100644 --- a/src/ontology/subsets/ro-developmental.tsv +++ b/src/ontology/subsets/ro-developmental.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid1 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid18 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid22 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid26 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid33 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid37 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid40 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid5 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid52 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid58 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid61 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid64 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid67 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid1 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid18 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid22 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid26 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid33 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid37 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid40 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid5 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid52 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid58 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid61 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid64 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid67 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid9 @@ -29,6 +29,7 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 + @@ -39,7 +40,6 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 - @@ -47,6 +47,8 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 + + diff --git a/src/ontology/subsets/ro-interaction.json b/src/ontology/subsets/ro-interaction.json index f20717da..63fc49ba 100644 --- a/src/ontology/subsets/ro-interaction.json +++ b/src/ontology/subsets/ro-interaction.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index 4ef159e2..122c9d98 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index cd814966..6c96e01f 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-interaction.tsv b/src/ontology/subsets/ro-interaction.tsv index 9b1bc3ad..8318d6a8 100644 --- a/src/ontology/subsets/ro-interaction.tsv +++ b/src/ontology/subsets/ro-interaction.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid1 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid18 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid22 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid26 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid33 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid37 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid40 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid5 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid52 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid58 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid61 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid64 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid67 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid1 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid18 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid22 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid26 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid33 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid37 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid40 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid5 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid52 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid58 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid61 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid64 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid67 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid9 @@ -29,6 +29,7 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 + @@ -39,7 +40,6 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 - @@ -47,6 +47,8 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 + + diff --git a/src/ontology/subsets/ro-mereotopology.json b/src/ontology/subsets/ro-mereotopology.json index b4fa7b87..d0fdda09 100644 --- a/src/ontology/subsets/ro-mereotopology.json +++ b/src/ontology/subsets/ro-mereotopology.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index b3bbb2c2..31d0bd7e 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 0fd2522d..b0654e52 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-mereotopology.tsv b/src/ontology/subsets/ro-mereotopology.tsv index 58250b17..87955ff5 100644 --- a/src/ontology/subsets/ro-mereotopology.tsv +++ b/src/ontology/subsets/ro-mereotopology.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid1 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid18 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid22 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid26 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid33 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid37 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid40 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid5 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid52 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid58 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid61 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid64 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid67 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid1 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid18 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid22 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid26 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid33 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid37 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid40 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid5 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid52 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid58 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid61 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid64 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid67 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid9 @@ -29,6 +29,7 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 + @@ -39,7 +40,6 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 - @@ -47,6 +47,8 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 + + diff --git a/src/ontology/subsets/ro-sequence.json b/src/ontology/subsets/ro-sequence.json index 10e06877..2cfc531b 100644 --- a/src/ontology/subsets/ro-sequence.json +++ b/src/ontology/subsets/ro-sequence.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index 37ac9123..bbbc3979 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index 985fe0d8..359bce8a 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-sequence.tsv b/src/ontology/subsets/ro-sequence.tsv index 80c67530..aabcd030 100644 --- a/src/ontology/subsets/ro-sequence.tsv +++ b/src/ontology/subsets/ro-sequence.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid1 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid18 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid22 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid26 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid33 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid37 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid40 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid5 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid52 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid58 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid61 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid64 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid67 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid1 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid18 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid22 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid26 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid33 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid37 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid40 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid5 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid52 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid58 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid61 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid64 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid67 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid9 @@ -29,6 +29,7 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 + @@ -39,7 +40,6 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 - @@ -47,6 +47,8 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 + + diff --git a/src/ontology/subsets/ro-time-interval.json b/src/ontology/subsets/ro-time-interval.json index ca09a23e..4acf12c3 100644 --- a/src/ontology/subsets/ro-time-interval.json +++ b/src/ontology/subsets/ro-time-interval.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 394d300d..54ead77f 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index 1d0ac69e..a8cde506 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-time-interval.tsv b/src/ontology/subsets/ro-time-interval.tsv index 58e569a4..dadfed7a 100644 --- a/src/ontology/subsets/ro-time-interval.tsv +++ b/src/ontology/subsets/ro-time-interval.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid1 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid18 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid22 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid26 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid33 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid37 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid40 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid5 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid52 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid58 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid61 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid64 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid67 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid1 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid18 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid22 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid26 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid33 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid37 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid40 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid5 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid52 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid58 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid61 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid64 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid67 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid9 @@ -29,6 +29,7 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 + @@ -39,7 +40,6 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 - @@ -47,6 +47,8 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 + + diff --git a/subsets/ro-biotic-interaction.json b/subsets/ro-biotic-interaction.json index 8309ba7d..9fd62d8e 100644 --- a/subsets/ro-biotic-interaction.json +++ b/subsets/ro-biotic-interaction.json @@ -736,6 +736,43 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008501", "lbl" : "epiphyte of", @@ -1021,6 +1058,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002641", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002635" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "subPropertyOf", @@ -1113,6 +1158,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "inverseOf", diff --git a/subsets/ro-biotic-interaction.obo b/subsets/ro-biotic-interaction.obo index 1f33ac3f..82eed56a 100644 --- a/subsets/ro-biotic-interaction.obo +++ b/subsets/ro-biotic-interaction.obo @@ -441,6 +441,26 @@ def: "inverse of intracellular endoparasite of" [] subset: RO:0002259 is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002802 +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: RO:0002454 ! has host + [Typedef] id: RO:0008501 name: epiphyte of diff --git a/subsets/ro-biotic-interaction.owl b/subsets/ro-biotic-interaction.owl index 9017b92f..2373adf8 100644 --- a/subsets/ro-biotic-interaction.owl +++ b/subsets/ro-biotic-interaction.owl @@ -7,6 +7,7 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> @@ -65,6 +66,12 @@ + + + + + + @@ -754,6 +761,34 @@ + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -822,5 +857,5 @@ - + diff --git a/subsets/ro-causal.json b/subsets/ro-causal.json index 22c6414d..995c9dab 100644 --- a/subsets/ro-causal.json +++ b/subsets/ro-causal.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index aae8993f..b2bf3775 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index 40bb5909..5284eca2 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-causal.tsv b/subsets/ro-causal.tsv index f63b8b06..958994a5 100644 --- a/subsets/ro-causal.tsv +++ b/subsets/ro-causal.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid1 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid18 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid22 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid26 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid33 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid37 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid40 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid5 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid52 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid58 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid61 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid64 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid67 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid1 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid18 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid22 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid26 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid33 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid37 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid40 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid5 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid52 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid58 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid61 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid64 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid67 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid9 @@ -29,6 +29,7 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 + @@ -39,7 +40,6 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 - @@ -47,6 +47,8 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 + + diff --git a/subsets/ro-chado.json b/subsets/ro-chado.json index a473678c..492b6f02 100644 --- a/subsets/ro-chado.json +++ b/subsets/ro-chado.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/subsets/ro-chado.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/subsets/ro-chado.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -1838,6 +1838,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -2572,12 +2575,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -5352,7 +5360,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -10143,6 +10151,43 @@ "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", @@ -11815,6 +11860,54 @@ "val" : "2022-09-26T06:08:01Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -12299,6 +12392,25 @@ "val" : "https://orcid.org/0000-0003-1909-9269" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017005", + "lbl" : "contains measured amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2999-0103" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-5714-991X" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -12710,6 +12822,63 @@ "val" : "https://orcid.org/0000-0002-4142-7153" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -14789,6 +14958,16 @@ "val" : "is defined by" } ] } + }, { + "id" : "https://orcid.org/0000-0001-6677-8489", + "lbl" : "Aleix Puig-Barbé", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0001-6677-8489" + } ] + } }, { "id" : "https://orcid.org/0000-0001-6996-0040", "lbl" : "Austin Meier", @@ -14829,6 +15008,16 @@ "val" : "data scientist" } ] } + }, { + "id" : "https://orcid.org/0000-0002-2999-0103", + "lbl" : "Jie Zheng", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-2999-0103)" + } ] + } }, { "id" : "https://orcid.org/0000-0002-4366-3088", "lbl" : "Pier Luigi Buttigieg", @@ -14839,6 +15028,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-5714-991X", + "lbl" : "Christian J Stoeckert", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-6601-2165", "lbl" : "Christopher J. Mungall", @@ -14899,6 +15098,26 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1813-6857", + "lbl" : "Pascale Gaudet", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Canadian biocurator" + } ] + } + }, { + "id" : "https://orcid.org/0000-0003-1909-9269", + "lbl" : "S. Clint Dowland", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-1909-9269" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1940-6740", "lbl" : "Anna Maria Masci", @@ -14909,6 +15128,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-3138-4118", + "lbl" : "Jorrit Poelen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "software/data engineer" + } ] + } }, { "id" : "https://orcid.org/0000-0003-4423-4370", "lbl" : "Charles Tapley Hoyt", @@ -15308,6 +15537,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -16780,6 +17013,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -17192,6 +17433,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -17360,6 +17609,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -18036,6 +18301,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003000", "pred" : "inverseOf", diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index fe43ab79..dd45dd89 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -1,19 +1,24 @@ format-version: 1.2 subsetdef: common_anatomy "" +subsetdef: efo_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: human_reference_atlas "" +subsetdef: pheno_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" +subsetdef: uberon_slim "" subsetdef: upper_level "" +subsetdef: vertebrate_core "" default-namespace: relationship ontology: ro/subsets/ro-chado.obo property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Typedef] id: BFO:0000050 @@ -312,8 +317,9 @@ is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 -name: regulates_in_other_organism +name: regulates_in_another_organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "regulates in other organism" EXACT [] is_a: RO:0002418 ! causally upstream of or within [Typedef] @@ -630,7 +636,7 @@ id: RO:0002131 name: overlaps def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -735,7 +741,7 @@ is_a: RO:0002323 ! mereotopologically related to id: RO:0002177 name: attached_to_part_of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -775,6 +781,7 @@ id: RO:0002202 name: develops_from def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -883,7 +890,7 @@ is_a: RO:0002216 ! capable of part of id: RO:0002216 name: capable_of_part_of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -1229,7 +1236,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 -name: results_in_formation_of +name: results_in_formation_of_anatomical_entity is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -1307,7 +1314,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002314 name: characteristic_of_part_of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -1373,7 +1380,7 @@ def: "A grouping relationship for any relationship directly involving a function id: RO:0002329 name: part_of_structure_that_is_capable_of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -1843,7 +1850,7 @@ id: RO:0002432 name: is_active_in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -2114,7 +2121,7 @@ is_a: RO:0002476 ! child nucleus of id: RO:0002479 name: has_part_that_occurs_in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 @@ -2280,7 +2287,7 @@ is_a: RO:0002566 ! causally influences id: RO:0002509 name: determined_by_part_of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -2618,12 +2625,12 @@ is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results_in_synthesis_of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 name: results_in_assembly_of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] @@ -2871,6 +2878,19 @@ def: "Two or more individuals sharing the same roost site (cave, mine, tree or t is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with +[Typedef] +id: RO:0002802 +name: reservoir_host_of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has_reservoir_host +def: "inverse of reservoir host of" [] +is_a: RO:0002454 ! has host + [Typedef] id: RO:0003000 name: produces @@ -3498,6 +3518,20 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of +[Typedef] +id: RO:0012013 +name: positively_regulates_in_another_organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "positively regulates in other organism" EXACT [] +is_a: RO:0002010 ! regulates in another organism + +[Typedef] +id: RO:0012014 +name: negatively_regulates_in_another_organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "negatively regulates in other organism" EXACT [] +is_a: RO:0002010 ! regulates in another organism + [Typedef] id: RO:0013001 name: has_synaptic_IO_in_region @@ -3681,6 +3715,11 @@ def: "A relation between entities in which one increases as the other decreases. is_symmetric: true is_a: RO:0002610 ! correlated with +[Typedef] +id: RO:0017005 +name: contains_measured_amount +def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] + [Typedef] id: RO:0018001 name: is_myristoyltransferase_activity @@ -3820,6 +3859,25 @@ name: confers_susceptibility_to_condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] is_a: RO:0003304 ! contributes to condition +[Typedef] +id: RO:0020101 +name: vessel_supplies_blood_to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +is_a: RO:0002178 ! supplies + +[Typedef] +id: RO:0020102 +name: vessel_drains_blood_from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +is_a: RO:0002179 ! drains + +[Typedef] +id: RO:0020103 +name: directly_supplies_and_drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +is_a: RO:0002178 ! supplies +is_a: RO:0002179 ! drains + [Typedef] id: RO:0040035 name: disease_relationship diff --git a/subsets/ro-chado.owl b/subsets/ro-chado.owl index 389234a4..76b4fd58 100644 --- a/subsets/ro-chado.owl +++ b/subsets/ro-chado.owl @@ -17,12 +17,11 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2023-08-18 + + 2024-02-13 @@ -38,12 +37,6 @@ - - - - - - @@ -1122,59 +1115,81 @@ Where we have an annotation assertion - + - + - + - + + + - + - + + + - + - + + + - + - + + + - + - + + + - + - + - + - + + + + + + + + + + + + + - + - + @@ -1472,23 +1487,6 @@ Where we have an annotation assertion - - - - - - - - - - - + @@ -4538,7 +4545,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results in formation of + results in formation of anatomical entity @@ -4985,6 +4992,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -8278,6 +8286,34 @@ the a supports either the existence of b, or the truth value of b. + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -9636,6 +9672,36 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + positively regulates in other organism + + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + negatively regulates in other organism + + negatively regulates in another organism + + + + @@ -10065,6 +10131,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. + A relation between a container and measurement datum that specifies the actual amount of material in the container. + + + contains measured amount + + + + @@ -10433,6 +10511,46 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + vessel supplies blood to + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + vessel drains blood from + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + directly supplies and drains + + + + @@ -12276,6 +12394,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0001-6677-8489 + Aleix Puig-Barbé + + + + + Researcher ORCID=0000-0001-6677-8489 + + + + + + Aleix Puig-Barbé + + + + + @@ -12360,6 +12499,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-2999-0103) + Jie Zheng + + + + + researcher (ORCID 0000-0002-2999-0103) + + + + + + Jie Zheng + + + + + @@ -12381,6 +12541,27 @@ binary, and takes no temporal argument. + + + + researcher + Christian J Stoeckert + + + + + researcher + + + + + + Christian J Stoeckert + + + + + @@ -12507,6 +12688,48 @@ binary, and takes no temporal argument. + + + + Canadian biocurator + Pascale Gaudet + + + + + Canadian biocurator + + + + + + Pascale Gaudet + + + + + + + + + Researcher ORCID=0000-0003-1909-9269 + S. Clint Dowland + + + + + Researcher ORCID=0000-0003-1909-9269 + + + + + + S. Clint Dowland + + + + + @@ -12528,6 +12751,27 @@ binary, and takes no temporal argument. + + + + software/data engineer + Jorrit Poelen + + + + + software/data engineer + + + + + + Jorrit Poelen + + + + + @@ -13003,28 +13247,28 @@ No imports /////////////////////////////////////////////////////////////////////////////////////// --> - + - + - + - + - + - + - + - + @@ -13033,15 +13277,6 @@ No imports - - - - - - - - - @@ -13065,8 +13300,8 @@ No imports - - + + @@ -13076,8 +13311,8 @@ No imports - - + + @@ -13087,8 +13322,8 @@ No imports - - + + @@ -13105,8 +13340,8 @@ No imports - - + + @@ -13123,8 +13358,8 @@ No imports - - + + @@ -13134,8 +13369,8 @@ No imports - - + + @@ -13145,8 +13380,8 @@ No imports - - + + @@ -13163,8 +13398,8 @@ No imports - - + + @@ -13181,8 +13416,8 @@ No imports - - + + @@ -13192,8 +13427,8 @@ No imports - - + + @@ -13203,8 +13438,8 @@ No imports - - + + @@ -13221,8 +13456,8 @@ No imports - - + + @@ -13239,8 +13474,8 @@ No imports - - + + @@ -13250,8 +13485,8 @@ No imports - - + + @@ -13266,8 +13501,8 @@ No imports - - + + @@ -13284,8 +13519,8 @@ No imports - - + + @@ -13295,8 +13530,8 @@ No imports - - + + @@ -13311,8 +13546,8 @@ No imports - - + + @@ -13329,8 +13564,8 @@ No imports - - + + @@ -13340,8 +13575,8 @@ No imports - - + + @@ -13356,8 +13591,8 @@ No imports - - + + @@ -13374,8 +13609,8 @@ No imports - - + + @@ -13385,8 +13620,8 @@ No imports - - + + @@ -13401,8 +13636,8 @@ No imports - - + + @@ -13419,8 +13654,8 @@ No imports - - + + @@ -13430,8 +13665,8 @@ No imports - - + + @@ -13446,8 +13681,8 @@ No imports - - + + @@ -13507,8 +13742,8 @@ No imports - - + + @@ -13518,8 +13753,8 @@ No imports - - + + @@ -13534,8 +13769,8 @@ No imports - - + + @@ -13551,8 +13786,8 @@ No imports - - + + @@ -13561,9 +13796,9 @@ No imports - - - + + + @@ -13577,9 +13812,9 @@ No imports - - - + + + @@ -13595,8 +13830,8 @@ No imports - - + + @@ -13605,9 +13840,9 @@ No imports - - - + + + @@ -13621,7 +13856,7 @@ No imports - + @@ -13722,5 +13957,5 @@ No imports - + diff --git a/subsets/ro-developmental.json b/subsets/ro-developmental.json index f4109945..d6d32493 100644 --- a/subsets/ro-developmental.json +++ b/subsets/ro-developmental.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index 1b9a7611..6518ba78 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index d5a7ed64..5f2ee16a 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-developmental.tsv b/subsets/ro-developmental.tsv index 2409aaef..3095b994 100644 --- a/subsets/ro-developmental.tsv +++ b/subsets/ro-developmental.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid1 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid18 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid22 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid26 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid33 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid37 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid40 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid5 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid52 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid58 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid61 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid64 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid67 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid1 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid18 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid22 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid26 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid33 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid37 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid40 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid5 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid52 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid58 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid61 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid64 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid67 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid9 @@ -29,6 +29,7 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 + @@ -39,7 +40,6 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 - @@ -47,6 +47,8 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 + + diff --git a/subsets/ro-interaction.json b/subsets/ro-interaction.json index f20717da..63fc49ba 100644 --- a/subsets/ro-interaction.json +++ b/subsets/ro-interaction.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index 4ef159e2..122c9d98 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index cd814966..6c96e01f 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-interaction.tsv b/subsets/ro-interaction.tsv index 9b1bc3ad..8318d6a8 100644 --- a/subsets/ro-interaction.tsv +++ b/subsets/ro-interaction.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid1 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid18 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid22 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid26 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid33 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid37 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid40 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid5 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid52 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid58 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid61 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid64 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid67 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid1 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid18 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid22 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid26 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid33 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid37 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid40 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid5 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid52 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid58 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid61 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid64 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid67 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid9 @@ -29,6 +29,7 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 + @@ -39,7 +40,6 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 - @@ -47,6 +47,8 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 + + diff --git a/subsets/ro-mereotopology.json b/subsets/ro-mereotopology.json index b4fa7b87..d0fdda09 100644 --- a/subsets/ro-mereotopology.json +++ b/subsets/ro-mereotopology.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index b3bbb2c2..31d0bd7e 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 0fd2522d..b0654e52 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-mereotopology.tsv b/subsets/ro-mereotopology.tsv index 58250b17..87955ff5 100644 --- a/subsets/ro-mereotopology.tsv +++ b/subsets/ro-mereotopology.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid1 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid18 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid22 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid26 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid33 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid37 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid40 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid5 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid52 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid58 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid61 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid64 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid67 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid1 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid18 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid22 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid26 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid33 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid37 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid40 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid5 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid52 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid58 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid61 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid64 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid67 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid9 @@ -29,6 +29,7 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 + @@ -39,7 +40,6 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 - @@ -47,6 +47,8 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 + + diff --git a/subsets/ro-sequence.json b/subsets/ro-sequence.json index 10e06877..2cfc531b 100644 --- a/subsets/ro-sequence.json +++ b/subsets/ro-sequence.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 37ac9123..bbbc3979 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index 985fe0d8..359bce8a 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-sequence.tsv b/subsets/ro-sequence.tsv index 80c67530..aabcd030 100644 --- a/subsets/ro-sequence.tsv +++ b/subsets/ro-sequence.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid1 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid18 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid22 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid26 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid33 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid37 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid40 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid5 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid52 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid58 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid61 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid64 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid67 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid1 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid18 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid22 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid26 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid33 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid37 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid40 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid5 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid52 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid58 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid61 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid64 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid67 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid9 @@ -29,6 +29,7 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 + @@ -39,7 +40,6 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 - @@ -47,6 +47,8 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 + + diff --git a/subsets/ro-time-interval.json b/subsets/ro-time-interval.json index ca09a23e..4acf12c3 100644 --- a/subsets/ro-time-interval.json +++ b/subsets/ro-time-interval.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 394d300d..54ead77f 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index 1d0ac69e..a8cde506 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-time-interval.tsv b/subsets/ro-time-interval.tsv index 58e569a4..dadfed7a 100644 --- a/subsets/ro-time-interval.tsv +++ b/subsets/ro-time-interval.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid1 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid18 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid22 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid26 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid33 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid37 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid40 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid5 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid52 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid58 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid61 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid64 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid67 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid1 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid18 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid22 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid26 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid33 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid37 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid40 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid5 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid52 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid58 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid61 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid64 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid67 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid9 @@ -29,6 +29,7 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 + @@ -39,7 +40,6 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 - @@ -47,6 +47,8 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 + +