diff --git a/core.json b/core.json index a801c5ff..bf95e5bc 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" : "2024-02-13" + "val" : "2024-04-24" }, { "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/2024-02-13/core.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-04-24/core.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", diff --git a/core.obo b/core.obo index ef9d44e4..f2b41d7a 100644 --- a/core.obo +++ b/core.obo @@ -1,9 +1,9 @@ format-version: 1.2 -data-version: ro/releases/2024-02-13/core.owl +data-version: ro/releases/2024-04-24/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 "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-24" xsd:string [Term] id: BFO:0000002 diff --git a/core.owl b/core.owl index 89595aca..93d456ab 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#"> - + - 2024-02-13 + 2024-04-24 https://github.com/oborel/obo-relations/wiki/ROCore diff --git a/ro-base.json b/ro-base.json index 25a78385..2c4860ca 100644 --- a/ro-base.json +++ b/ro-base.json @@ -16,115 +16,14 @@ "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-02-13" + "val" : "2024-04-24" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro-base.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-04-24/ro-base.json" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/BFO_0000002", - "lbl" : "continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000003", - "lbl" : "occurrent", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000004", - "lbl" : "independent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - }, - "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000006", - "lbl" : "spatial region", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000015", - "lbl" : "process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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])" - }, - "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000016", - "lbl" : "disposition", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000017", - "lbl" : "realizable entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000019", - "lbl" : "quality", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000020", - "lbl" : "specifically dependent continuant", - "type" : "CLASS", - "meta" : { - "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." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000023", - "lbl" : "role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000031", - "lbl" : "generically dependent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" - }, - "comments" : [ "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "lbl" : "function", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000040", - "lbl" : "material entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." - } - } - }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", "lbl" : "part of", "type" : "PROPERTY", @@ -386,26 +285,6 @@ "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000141", - "lbl" : "immaterial entity", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000112", - "lbl" : "example of usage", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000426", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", "lbl" : "characteristic of", @@ -3493,11 +3372,11 @@ "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" } ] } }, { @@ -6053,6 +5932,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6077,6 +5959,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6313,6 +6198,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -6473,6 +6361,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -6484,6 +6375,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -6498,6 +6392,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -7840,6 +7737,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -7851,6 +7751,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -10055,6 +9958,41 @@ "val" : "https://orcid.org/0000-0002-8844-9165" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009006", + "lbl" : "assay measures characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8844-9165" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-05-23T15:24:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009007", + "lbl" : "characteristic measured by assay", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'assay measures characteristic'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8844-9165" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-05-23T15:29:50Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -11059,18 +10997,18 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" @@ -11127,6 +11065,82 @@ "val" : "https://orcid.org/0000-0002-5714-991X" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017006", + "lbl" : "has maximum capacity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube has maximum capacity 10 ml." + }, { + "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_0017008", + "lbl" : "owns", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A primitive relation that holds between entities x and y in which y is at x's full disposal." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "biobank organization owns a specimen" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "hospital owns a laboratory facility" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1834-3856" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-03-29T16:57:03Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017009", + "lbl" : "is owned by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of the owns relation." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "freezer is owned by a biobank organization" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1834-3856" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-03-29T17:06:06Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -11595,6 +11609,40 @@ "val" : "2024-02-01T10:09:59Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -13500,174 +13548,8 @@ "val" : "http://purl.obolibrary.org/obo/HOM_0000075" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "lbl" : "valid_for_go_annotation_extension", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:05:29Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", - "lbl" : "valid_for_go_gp2term", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:05:18Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "lbl" : "valid_for_go_ontology", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:04:12Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", - "lbl" : "valid_for_gocam", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:05:45Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", - "lbl" : "eco subset", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" - } ] - } - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", - "lbl" : "subset_property", - "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", - "lbl" : "has_broad_synonym", - "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", - "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", - "lbl" : "has_exact_synonym", - "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", - "lbl" : "has_narrow_synonym", - "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", - "lbl" : "has_obo_format_version", - "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", - "lbl" : "has_related_synonym", - "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", - "lbl" : "in_subset", - "type" : "PROPERTY" - }, { - "id" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "is defined by" - } ] - } } ], "edges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000016", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000023", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000034", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000040", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000141", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "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_0002532", "pred" : "http://purl.obolibrary.org/obo/RO_0002524", "obj" : "http://purl.obolibrary.org/obo/RO_0002533" @@ -14938,7 +14820,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -14982,15 +14864,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002472", "pred" : "subPropertyOf", @@ -16167,6 +16049,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -16895,6 +16785,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008507", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008508" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0009006", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0009007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0010001", "pred" : "inverseOf", @@ -16919,6 +16813,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0015001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0015002" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0017008", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0017009" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0018002", "pred" : "inverseOf", @@ -16933,59 +16831,6 @@ "obj" : "http://purl.obolibrary.org/obo/RO_0018034" } ], "domainRangeAxioms" : [ { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "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_0000017", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" - } ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002214", - "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/RO_0002214", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", - "pred" : "http://purl.obolibrary.org/obo/RO_0002214", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" - } ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_HOM0000000", - "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", - "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" - } ] - }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] @@ -17413,6 +17258,14 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0009004", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009006", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000070" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009007", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000070" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -17493,6 +17346,10 @@ "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_0017006", + "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" ], @@ -17509,6 +17366,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 f5733cdf..189abd20 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -1,130 +1,12 @@ format-version: 1.2 -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 "" -subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" -subsetdef: ro-eco "" -subsetdef: RO:0002259 "" +data-version: ro/releases/2024-04-24/ro-base.owl ontology: ro/ro-base property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 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 "2024-02-13" xsd:string - -[Term] -id: BFO:0000002 -name: continuant -def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] -disjoint_from: BFO:0000003 ! occurrent -relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant -relationship: RO:0002214 BFO:0000002 {all_only="true"} ! has prototype continuant -relationship: RO:HOM0000000 BFO:0000002 {all_only="true"} ! continuant - -[Term] -id: BFO:0000003 -name: occurrent -def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent -relationship: RO:HOM0000000 BFO:0000003 {all_only="true"} ! occurrent - -[Term] -id: BFO:0000004 -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:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant - -[Term] -id: BFO:0000006 -name: spatial region -is_a: BFO:0000141 ! immaterial entity - -[Term] -id: BFO:0000015 -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: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process - -[Term] -id: BFO:0000016 -name: disposition -is_a: BFO:0000017 ! realizable entity -disjoint_from: BFO:0000023 ! role - -[Term] -id: BFO:0000017 -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 -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 -relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality - -[Term] -id: BFO:0000020 -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 - -[Term] -id: BFO:0000023 -name: role -def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] -is_a: BFO:0000017 ! realizable entity - -[Term] -id: BFO:0000031 -name: generically dependent continuant -def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] -comment: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. -is_a: BFO:0000002 ! continuant -relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant - -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition - -[Term] -id: BFO:0000040 -name: material entity -def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] -is_a: BFO:0000004 ! independent continuant -disjoint_from: BFO:0000141 ! immaterial entity - -[Term] -id: BFO:0000141 -name: immaterial entity -is_a: BFO:0000004 ! independent continuant - -[Term] -id: CHEBI:50906 -is_a: PATO:0000001 - -[Term] -id: GO:0004842 - -[Term] -id: GO:0016301 - -[Term] -id: GO:0019107 +property_value: owl:versionInfo "2024-04-24" xsd:string [Term] id: RO:0002310 @@ -166,7 +48,7 @@ property_value: IAO:0000232 "Sequence bearers can be molecular entities, such as id: RO:0002577 name: system def: "A material entity consisting of multiple components that are causally integrated." [] -is_a: BFO:0000040 ! material entity +is_a: BFO:0000040 property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.jbiomedsem.com/content/4/1/43" xsd:string @@ -234,8 +116,8 @@ property_value: IAO:0000118 "is realized by" xsd:string property_value: IAO:0000118 "realized_in" xsd:string property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000017 ! realizable entity -range: BFO:0000015 ! process +domain: BFO:0000017 +range: BFO:0000015 inverse_of: BFO:0000055 ! realizes [Typedef] @@ -248,8 +130,8 @@ property_value: IAO:0000112 "this investigation realizes this investigator role" property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl -domain: BFO:0000015 ! process -range: BFO:0000017 ! realizable entity +domain: BFO:0000015 +range: BFO:0000017 [Typedef] id: BFO:0000060 @@ -268,8 +150,8 @@ property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string property_value: IAO:0000118 "preceded_by" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 holds_over_chain: BFO:0000050 BFO:0000062 holds_over_chain: RO:0002091 BFO:0000062 holds_over_chain: RO:0002092 BFO:0000062 @@ -283,8 +165,8 @@ name: precedes def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco property_value: IAO:0000111 "precedes" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 holds_over_chain: BFO:0000050 BFO:0000063 holds_over_chain: RO:0002092 BFO:0000063 is_transitive: true @@ -304,8 +186,8 @@ property_value: IAO:0000118 "unfolds in" xsd:string 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 -range: BFO:0000004 ! independent continuant +domain: BFO:0000003 +range: BFO:0000004 holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process transitive_over: BFO:0000050 ! part of @@ -343,7 +225,7 @@ 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 -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 is_inverse_functional: true [Typedef] @@ -355,8 +237,8 @@ property_value: IAO:0000112 "this blood clot participates in this blood coagulat property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string property_value: IAO:0000118 "participates_in" xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000003 ! occurrent +domain: BFO:0000002 +range: BFO:0000003 inverse_of: RO:0000057 ! has participant [Typedef] @@ -370,8 +252,8 @@ property_value: IAO:0000112 "this investigation has participant this investigato property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string 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 -range: BFO:0000002 ! continuant +domain: BFO:0000003 +range: BFO:0000002 holds_over_chain: BFO:0000051 RO:0000057 [Typedef] @@ -380,8 +262,8 @@ name: is concretized as def: "A relationship between a generically dependent continuant and a specifically 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. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] 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 +domain: BFO:0000031 +range: BFO:0000020 inverse_of: RO:0000059 ! concretizes [Typedef] @@ -390,8 +272,8 @@ 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 -range: BFO:0000031 ! generically dependent continuant +domain: BFO:0000020 +range: BFO:0000031 [Typedef] id: RO:0000079 @@ -402,7 +284,7 @@ property_value: IAO:0000112 "this catalysis function is a function of this enzym property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string -domain: BFO:0000034 ! function +domain: BFO:0000034 is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -437,8 +319,8 @@ def: "a relation between an independent continuant (the bearer) and a function, property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "has_function" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000034 ! function +domain: BFO:0000004 +range: BFO:0000034 is_a: RO:0000053 ! has characteristic [Typedef] @@ -448,7 +330,7 @@ def: "a relation between an independent continuant (the bearer) and a quality, i property_value: IAO:0000112 "this apple has quality this red color" xsd:string property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string property_value: IAO:0000118 "has_quality" xsd:string -range: BFO:0000019 ! quality +range: BFO:0000019 is_a: RO:0000053 ! has characteristic [Typedef] @@ -458,16 +340,16 @@ def: "a relation between an independent continuant (the bearer) and a role, in w property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "has_role" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000023 ! role +domain: BFO:0000004 +range: BFO:0000023 is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000091 name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] -domain: BFO:0000004 ! independent continuant -range: BFO:0000016 ! disposition +domain: BFO:0000004 +range: BFO:0000016 is_a: RO:0000053 ! has characteristic inverse_of: RO:0000092 ! disposition of @@ -571,7 +453,7 @@ id: RO:0001020 name: is allergic trigger for def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string -domain: BFO:0000040 ! material entity +domain: BFO:0000040 is_a: RO:0003302 ! causes or contributes to condition inverse_of: RO:0001022 ! has allergic trigger @@ -579,7 +461,7 @@ inverse_of: RO:0001022 ! has allergic trigger id: RO:0001021 name: is autoimmune trigger for def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] -domain: BFO:0000040 ! material entity +domain: BFO:0000040 is_a: RO:0003302 ! causes or contributes to condition inverse_of: RO:0001023 ! has autoimmune trigger @@ -588,14 +470,14 @@ id: RO:0001022 name: has allergic trigger def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string -range: BFO:0000040 ! material entity +range: BFO:0000040 is_a: RO:0003302 ! causes or contributes to condition [Typedef] id: RO:0001023 name: has autoimmune trigger def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] -range: BFO:0000040 ! material entity +range: BFO:0000040 is_a: RO:0003302 ! causes or contributes to condition [Typedef] @@ -612,8 +494,8 @@ 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 {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 +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."} +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."} is_transitive: true transitive_over: BFO:0000050 ! part of @@ -653,8 +535,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has boundary" xsd:string property_value: IAO:0000118 "has_2D_boundary" xsd:string property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000141 ! immaterial entity +domain: BFO:0000040 +range: BFO:0000141 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -698,7 +580,7 @@ def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\ comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -range: BFO:0000040 ! material entity +range: BFO:0000040 is_a: BFO:0000050 ! part of [Typedef] @@ -727,8 +609,8 @@ def: "x 'regulates in other organism' y if and only if: (x is the realization of 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 +domain: BFO:0000015 +range: BFO:0000015 is_a: RO:0002418 ! causally upstream of or within [Typedef] @@ -743,8 +625,8 @@ holds_over_chain: RO:0002211 RO:0002313 id: RO:0002012 name: occurrent part of def: "A part of relation that applies only between occurrents." [] -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 is_a: BFO:0000050 ! part of is_a: RO:0002418 ! causally upstream of or within @@ -798,8 +680,8 @@ creation_date: 2017-05-24T09:44:33Z id: RO:0002018 name: has component process def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -domain: BFO:0000015 ! process -range: BFO:0000015 ! process +domain: BFO:0000015 +range: BFO:0000015 is_a: RO:0002180 ! has component created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z @@ -982,8 +864,8 @@ comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "io" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 is_a: RO:0002222 ! temporally related to [Typedef] @@ -1172,7 +1054,7 @@ name: releases neurotransmitter property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string domain: UBERON:0000061 -range: BFO:0000040 ! material entity +range: BFO:0000040 [Typedef] id: RO:0002112 @@ -1314,8 +1196,8 @@ property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "FMA:85972" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant +domain: BFO:0000004 +range: BFO:0000004 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -1442,7 +1324,7 @@ property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -domain: BFO:0000004 ! independent continuant +domain: BFO:0000004 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -1515,8 +1397,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant +domain: BFO:0000004 +range: BFO:0000004 is_transitive: true is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by @@ -1543,8 +1425,8 @@ def: "definition \"x has gene product of y if and only if y is a gene (SO:000070 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000004 ! independent continuant -range: BFO:0000002 ! continuant +domain: BFO:0000004 +range: BFO:0000002 holds_over_chain: RO:0002512 RO:0002510 is_a: RO:0002330 ! genomically related to inverse_of: RO:0002205 ! has gene product @@ -1557,8 +1439,8 @@ property_value: IAO:0000112 "every HOTAIR lncRNA is the gene product of some HOX property_value: IAO:0000112 "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000002 ! continuant -range: BFO:0000004 ! independent continuant +domain: BFO:0000002 +range: BFO:0000004 holds_over_chain: RO:0002511 RO:0002513 is_a: RO:0002330 ! genomically related to @@ -1569,7 +1451,7 @@ def: "x expressed in y if and only if there is a gene expression process (GO:001 property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000002 ! continuant +domain: BFO:0000002 range: UBERON:0000465 is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses @@ -1627,8 +1509,8 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean -domain: BFO:0000015 ! process -range: BFO:0000015 ! process +domain: BFO:0000015 +range: BFO:0000015 holds_over_chain: RO:0002230 RO:0002211 holds_over_chain: RO:0002578 RO:0002578 is_transitive: true @@ -1694,8 +1576,8 @@ property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process +domain: BFO:0000004 +range: BFO:0000015 is_a: RO:0002216 ! capable of part of [Typedef] @@ -1753,8 +1635,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant +domain: BFO:0000004 +range: BFO:0000004 is_a: RO:0002163 ! spatially disjoint from [Typedef] @@ -1777,8 +1659,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 [Typedef] id: RO:0002223 @@ -1873,8 +1755,8 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string -domain: BFO:0000015 ! process -range: BFO:0000004 ! independent continuant +domain: BFO:0000015 +range: BFO:0000004 holds_over_chain: RO:0002224 BFO:0000066 is_a: RO:0002479 ! has part that occurs in @@ -1886,8 +1768,8 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string -domain: BFO:0000015 ! process -range: BFO:0000004 ! independent continuant +domain: BFO:0000015 +range: BFO:0000004 holds_over_chain: RO:0002230 BFO:0000066 is_a: RO:0002479 ! has part that occurs in @@ -1903,7 +1785,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI -domain: BFO:0000015 ! process +domain: BFO:0000015 holds_over_chain: RO:0002224 RO:0002233 is_a: RO:0000057 ! has participant inverse_of: RO:0002352 ! input of @@ -1946,7 +1828,7 @@ is_a: RO:0002444 ! parasite of id: RO:0002238 name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: RO:0000057 ! has participant @@ -2005,8 +1887,8 @@ def: "A relationship that holds between a substance and a chemical entity, if th synonym: "has active pharmaceutical ingredient" RELATED [] synonym: "has active substance" EXACT [] property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: BFO:0000051 ! has part inverse_of: RO:0002249 ! active ingredient in @@ -2096,8 +1978,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant +domain: BFO:0000002 +range: BFO:0000002 is_a: RO:0002324 ! developmentally related to inverse_of: RO:0002286 ! developmentally succeeded by @@ -2437,8 +2319,8 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -2496,8 +2378,8 @@ name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant +domain: BFO:0000002 +range: BFO:0000002 [Typedef] id: RO:0002331 @@ -2520,8 +2402,8 @@ property_value: IAO:0000112 "every cellular sphingolipid homeostasis process reg property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string -domain: BFO:0000015 ! process -range: BFO:0000040 ! material entity +domain: BFO:0000015 +range: BFO:0000040 is_a: RO:0002328 ! functionally related to [Typedef] @@ -2541,8 +2423,8 @@ def: "inverse of regulates" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string -domain: BFO:0000015 ! process -range: BFO:0000015 ! process +domain: BFO:0000015 +range: BFO:0000015 is_transitive: true is_a: RO:0002427 ! causally downstream of or within @@ -2568,8 +2450,8 @@ name: related via localization to def: "A relationship that holds via some process of localization" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string -domain: BFO:0000015 ! process -range: BFO:0000002 ! continuant +domain: BFO:0000015 +range: BFO:0000002 [Typedef] id: RO:0002338 @@ -2798,8 +2680,8 @@ property_value: IAO:0000232 "This relation can be used for geographic features ( property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -3096,8 +2978,8 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string -domain: BFO:0000015 ! process -range: BFO:0000015 ! process +domain: BFO:0000015 +range: BFO:0000015 is_transitive: true is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -3131,7 +3013,7 @@ 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 is_a: RO:0002424 ! differs in [Typedef] @@ -3217,8 +3099,8 @@ property_value: IAO:0000116 "This relation and all sub-relations can be applied property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_symmetric: true [Typedef] @@ -3252,8 +3134,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_symmetric: true is_a: RO:0002321 ! ecologically related to is_a: RO:0002434 ! interacts with @@ -3326,6 +3208,7 @@ is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002444 name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string @@ -3339,6 +3222,7 @@ inverse_of: RO:0002445 ! parasitized by [Typedef] id: RO:0002445 name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3374,8 +3258,8 @@ def: "The entity A, immediately upstream of the entity B, has an activity that r synonym: "molecularly controls" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002436 ! molecularly interacts with is_a: RO:0011002 ! regulates activity of @@ -3387,8 +3271,8 @@ synonym: "molecularly decreases activity of" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002448 ! directly regulates activity of [Typedef] @@ -3399,8 +3283,8 @@ synonym: "molecularly increases activity of" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002448 ! directly regulates activity of [Typedef] @@ -3462,10 +3346,11 @@ is_a: RO:0002442 ! mutualistically interacts with [Typedef] id: RO:0002457 name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with inverse_of: RO:0002469 ! provides nutrients for [Typedef] @@ -3552,26 +3437,29 @@ is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002469 name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002470 name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002471 name: is eaten by +def: "Inverse of eats" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002472 @@ -3591,8 +3479,8 @@ property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: BFO:0000051 ! has part [Typedef] @@ -3626,8 +3514,8 @@ 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." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant +domain: BFO:0000003 +range: BFO:0000004 holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] @@ -3670,8 +3558,8 @@ id: RO:0002487 name: relation between physical entity and a process or stage property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000003 ! occurrent +domain: BFO:0000004 +range: BFO:0000003 [Typedef] id: RO:0002488 @@ -3785,8 +3673,8 @@ def: "p is causally related to q if and only if p or any part of p and q or any property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 is_a: RO:0002410 ! causally related to [Typedef] @@ -3821,8 +3709,8 @@ property_value: IAO:0000116 "The intent is that the process branch of the causal property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant +domain: BFO:0000002 +range: BFO:0000002 is_a: RO:0002410 ! causally related to [Typedef] @@ -3838,7 +3726,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 ! system -range: BFO:0000040 ! material entity +range: BFO:0000040 is_a: BFO:0000050 ! part of is_a: RO:0002509 ! determined by part of is_a: RO:0002559 ! causally influenced by @@ -3861,7 +3749,7 @@ def: "s 'determined by part of' w if and only if there exists some f such that ( subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system -range: BFO:0000040 ! material entity +range: BFO:0000040 holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -4167,6 +4055,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002556 name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002454 ! has host @@ -4175,6 +4064,7 @@ inverse_of: RO:0002557 ! has pathogen [Typedef] id: RO:0002557 name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002453 ! host of @@ -4232,8 +4122,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant +domain: BFO:0000002 +range: BFO:0000002 is_a: RO:0002506 ! causal relation between entities [Typedef] @@ -4273,8 +4163,8 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002131 ! overlaps [Typedef] @@ -4284,7 +4174,7 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000040 ! material entity +range: BFO:0000040 is_a: BFO:0000050 ! part of [Typedef] @@ -4293,7 +4183,7 @@ name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000141 ! immaterial entity +domain: BFO:0000141 is_a: RO:0002571 ! lumen of [Typedef] @@ -4304,8 +4194,8 @@ 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 +range: BFO:0000020 [Typedef] id: RO:0002574 @@ -4421,8 +4311,8 @@ def: "A relationship that holds between a material entity and a process in which property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -domain: BFO:0000040 ! material entity -range: BFO:0000015 ! process +domain: BFO:0000040 +range: BFO:0000015 is_a: RO:0002410 ! causally related to [Typedef] @@ -4710,8 +4600,8 @@ comment: Note that this definition doesn't quite distinguish the output of a tra subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 inverse_of: RO:0003001 ! produced by [Typedef] @@ -4721,16 +4611,16 @@ def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 [Typedef] id: RO:0003002 name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002449 ! directly negatively regulates activity of [Typedef] @@ -4738,8 +4628,8 @@ id: RO:0003003 name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002450 ! directly positively regulates activity of [Typedef] @@ -4822,7 +4712,7 @@ is_a: RO:0002410 ! causally related to id: RO:0004000 name: condition has genetic basis in property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string -domain: BFO:0000017 ! realizable entity +domain: BFO:0000017 is_a: RO:0002410 ! causally related to inverse_of: RO:0004010 ! is genetic basis for condition created_by: https://orcid.org/0000-0002-6601-2165 @@ -4913,7 +4803,7 @@ creation_date: 2018-12-13T11:26:56Z id: RO:0004010 name: is genetic basis for condition property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string -range: BFO:0000017 ! realizable entity +range: BFO:0000017 is_a: RO:0004018 ! is basis for realizable created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z @@ -5014,7 +4904,7 @@ id: RO:0004021 name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string -range: BFO:0000015 ! process +range: BFO:0000015 is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z @@ -5045,7 +4935,7 @@ name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string domain: OGMS:0000031 -range: BFO:0000015 ! process +range: BFO:0000015 holds_over_chain: RO:0004025 RO:0002215 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of @@ -5070,7 +4960,7 @@ def: "A relationship between a disease and an anatomical entity where the diseas property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string domain: OGMS:0000031 -range: BFO:0000004 ! independent continuant +range: BFO:0000004 is_a: RO:0040035 ! disease relationship created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z @@ -5080,7 +4970,7 @@ id: RO:0004027 name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] domain: OGMS:0000031 -range: BFO:0000004 ! independent continuant +range: BFO:0000004 is_a: RO:0004026 ! disease has location created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z @@ -5089,8 +4979,8 @@ creation_date: 2017-12-26T19:37:31Z id: RO:0004028 name: realized in response to stimulus def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] -domain: BFO:0000017 ! realizable entity -range: BFO:0000040 ! material entity +domain: BFO:0000017 +range: BFO:0000040 holds_over_chain: RO:0009501 RO:0002233 is_a: RO:0002410 ! causally related to created_by: https://orcid.org/0000-0002-6601-2165 @@ -5296,8 +5186,8 @@ property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xs property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 [Typedef] id: RO:0009002 @@ -5306,8 +5196,8 @@ def: "\"has substance removed\" is a relation existing between two physical enti property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 [Typedef] id: RO:0009003 @@ -5316,8 +5206,8 @@ def: "\"immersed in\" is a relation between a (physical) entity and a fluid subs property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 [Typedef] id: RO:0009004 @@ -5326,7 +5216,7 @@ def: "'has consumer' is a relation between a material entity and an organism in property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 -domain: BFO:0000040 ! material entity +domain: BFO:0000040 range: OBI:0100026 [Typedef] @@ -5338,6 +5228,26 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 is_a: RO:0009001 ! has substance added +[Typedef] +id: RO:0009006 +name: assay measures characteristic +def: "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 +property_value: http://purl.org/dc/terms/date "2023-05-23T15:24:15Z" xsd:dateTime +property_value: IAO:0000112 "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material." xsd:string +domain: OBI:0000070 +range: BFO:0000020 +inverse_of: RO:0009007 ! characteristic measured by assay + +[Typedef] +id: RO:0009007 +name: characteristic measured by assay +def: "Inverse of 'assay measures characteristic'" [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 +property_value: http://purl.org/dc/terms/date "2023-05-23T15:29:50Z" xsd:dateTime +domain: BFO:0000020 +range: OBI:0000070 + [Typedef] id: RO:0009501 name: realized in response to @@ -5351,8 +5261,8 @@ property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI -domain: BFO:0000017 ! realizable entity -range: BFO:0000015 ! process +domain: BFO:0000017 +range: BFO:0000015 holds_over_chain: BFO:0000054 RO:0002404 is_a: RO:0002410 ! causally related to @@ -5367,8 +5277,8 @@ property_value: IAO:0000112 "The pattern shared by chess boards generically depe property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string property_value: IAO:0000119 "[072-ISO]" xsd:string -domain: BFO:0000031 ! generically dependent continuant -range: BFO:0000004 ! independent continuant +domain: BFO:0000031 +range: BFO:0000004 holds_over_chain: RO:0000052 RO:0000058 inverse_of: RO:0010002 ! is carrier of @@ -5380,8 +5290,8 @@ property_value: IAO:0000112 "Molecules of DNA are carriers of genetic informatio property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string property_value: IAO:0000119 "[072-ISO]" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000031 ! generically dependent continuant +domain: BFO:0000004 +range: BFO:0000031 holds_over_chain: RO:0000059 RO:0000053 [Typedef] @@ -5389,8 +5299,8 @@ id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002566 ! causally influences [Typedef] @@ -5398,8 +5308,8 @@ id: RO:0011003 name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002566 ! causally influences [Typedef] @@ -5407,8 +5317,8 @@ id: RO:0011004 name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0011002 ! regulates activity of [Typedef] @@ -5416,8 +5326,8 @@ id: RO:0011007 name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0011023 ! indirectly negatively regulates quantity of [Typedef] @@ -5425,8 +5335,8 @@ id: RO:0011008 name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0011024 ! indirectly positively regulates quantity of [Typedef] @@ -5434,8 +5344,8 @@ id: RO:0011009 name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0011021 ! directly regulates quantity of [Typedef] @@ -5443,8 +5353,8 @@ id: RO:0011010 name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0011021 ! directly regulates quantity of [Typedef] @@ -5453,8 +5363,8 @@ name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0011004 ! indirectly regulates activity of [Typedef] @@ -5463,8 +5373,8 @@ name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0011010 ! directly negatively regulates quantity of [Typedef] @@ -5473,8 +5383,8 @@ name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0011009 ! directly positively regulates quantity of [Typedef] @@ -5888,9 +5798,9 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: RO:0002215 RO:0002233 @@ -5924,6 +5834,40 @@ property_value: IAO:0000112 "anticoagulant-containing test tube contains measure domain: OBI:0000967 range: COB:0000121 +[Typedef] +id: RO:0017006 +name: has maximum capacity +def: "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." [] +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 has maximum capacity 10 ml." xsd:string +domain: OBI:0000967 +range: COB:0000121 + +[Typedef] +id: RO:0017008 +name: owns +def: "A primitive relation that holds between entities x and y in which y is at x's full disposal." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1834-3856 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: http://purl.org/dc/terms/description "This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal." xsd:string +property_value: IAO:0000112 "biobank organization owns a specimen" xsd:string +property_value: IAO:0000112 "hospital owns a laboratory facility" xsd:string +inverse_of: RO:0017009 ! is owned by +creation_date: 2023-03-29T16:57:03Z + +[Typedef] +id: RO:0017009 +name: is owned by +def: "Inverse of the owns relation." [] +subset: RO:0002259 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1834-3856 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: IAO:0000112 "freezer is owned by a biobank organization" xsd:string +creation_date: 2023-03-29T17:06:06Z + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -6099,7 +6043,7 @@ id: RO:0019000 name: regulates characteristic def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 -domain: BFO:0000015 ! process +domain: BFO:0000015 range: PATO:0000001 holds_over_chain: RO:0002211 RO:0019000 is_a: RO:0002410 ! causally related to @@ -6162,6 +6106,26 @@ range: UBERON:0000061 is_a: RO:0002178 ! supplies is_a: RO:0002179 ! drains +[Typedef] +id: RO:0020202 +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0020203 +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: BFO:0000051 ! has part + [Typedef] id: RO:0040035 name: disease relationship diff --git a/ro-base.owl b/ro-base.owl index b64dfefc..266c2069 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -13,17 +13,16 @@ xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" 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: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 - 2024-02-13 + 2024-04-24 https://github.com/oborel/obo-relations/ @@ -48,9 +47,7 @@ - - example of usage - + @@ -62,9 +59,7 @@ - - definition - + @@ -112,10 +107,7 @@ - - An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. - - + @@ -306,7 +298,6 @@ WHERE { defined by inverse - @@ -327,7 +318,6 @@ WHERE { An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. annotation property cardinality - @@ -859,64 +849,6 @@ Where we have an annotation assertion - - - - - 2020-09-22T11:05:29Z - valid_for_go_annotation_extension - - - - - - - - - - - 2020-09-22T11:05:18Z - valid_for_go_gp2term - - - - - - - - - - - 2020-09-22T11:04:12Z - valid_for_go_ontology - - - - - - - - - - - 2020-09-22T11:05:45Z - valid_for_gocam - - - - - - - - - - eco subset - - - - - - @@ -977,20 +909,6 @@ Where we have an annotation assertion - - - - - - - - - - subset_property - - - - @@ -1003,109 +921,39 @@ Where we have an annotation assertion - - - - - - - - has_broad_synonym - + - - database_cross_reference - + - - has_exact_synonym - + - - has_narrow_synonym - - - - - - - - has_obo_format_version - + - - has_related_synonym - - - - - - - + - - in_subset - - - - - - - - - - - - - - - - - - - - is defined by - - - - - is defined by - This is an experimental annotation - - - - - - - - - - - - - + @@ -1115,12 +963,6 @@ Where we have an annotation assertion - - - - - - @@ -4025,10 +3867,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + has component participant @@ -5123,7 +4965,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - has member is a mereological relation between a collection and an item. SIO @@ -6188,6 +6029,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes direct parasite of @@ -6203,6 +6045,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -6396,8 +6239,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. @@ -6534,7 +6378,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. provides nutrients for @@ -6545,7 +6390,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with @@ -6557,7 +6403,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -7453,7 +7300,6 @@ the a supports either the existence of b, or the truth value of b. - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' @@ -7545,6 +7391,7 @@ the a supports either the existence of b, or the truth value of b. + Inverse of has pathogen pathogen of @@ -7556,6 +7403,7 @@ the a supports either the existence of b, or the truth value of b. + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member has pathogen @@ -8436,7 +8284,6 @@ the a supports either the existence of b, or the truth value of b. - A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. is used to study @@ -9324,7 +9171,6 @@ Environmental exposures include those imposed by natural environments, experimen - muffin 'has substance added' some 'baking soda' @@ -9340,7 +9186,6 @@ Environmental exposures include those imposed by natural environments, experimen - 'egg white' 'has substance removed' some 'egg yolk' @@ -9355,7 +9200,6 @@ Environmental exposures include those imposed by natural environments, experimen - sardines 'immersed in' some 'oil and mustard' @@ -9385,7 +9229,6 @@ Environmental exposures include those imposed by natural environments, experimen - bread 'has primary substance added' some 'flour' 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. @@ -9395,6 +9238,34 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material. + A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic. + + 2023-05-23T15:24:15Z + assay measures characteristic + + + + + + + + + + Inverse of 'assay measures characteristic' + + 2023-05-23T15:29:50Z + characteristic measured by assay + + + + @@ -10269,10 +10140,10 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 + + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -10298,7 +10169,6 @@ For example, protein A (transcription factor) indirectly increases by expression - A relation between entities in which one increases as the other decreases. inversely correlated with @@ -10321,6 +10191,52 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + anticoagulant-containing test tube has maximum capacity 10 ml. + A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume. + + + has maximum capacity + + + + + + + + + biobank organization owns a specimen + hospital owns a laboratory facility + A primitive relation that holds between entities x and y in which y is at x's full disposal. + + + + This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal. + 2023-03-29T16:57:03Z + owns + + + + + + + + freezer is owned by a biobank organization + Inverse of the owns relation. + + + + 2023-03-29T17:06:06Z + + is owned by + + + + @@ -10737,6 +10653,34 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + A relationship between a ratio or proportion and its dividend. + + has dividend + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + has divisor + has denominator + + + + @@ -12427,33 +12371,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - - - - - - - - - - - - - - - - - - - - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - continuant @@ -12461,184 +12384,85 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - - - - - - - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. - occurrent - - - - - - - - - - - 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]) - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - independent continuant - + - - - spatial region - + - - - - - - - - - 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]) - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - process - + - - - - disposition - + - - - - - - - - - - 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 entity - + - - - - - - - - - quality - + - - - - - - - - - - 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. - specifically dependent continuant - + - - - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - role - + - - - - - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - generically dependent continuant - + - - - function - + - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity @@ -12646,22 +12470,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - - immaterial entity - - - - - - - - @@ -12708,25 +12522,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - - - - - - - - - - - - - true - - - - - - @@ -12739,29 +12534,9 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - - - - - - - true - - - - - - - + - - - - - true - - - + @@ -12801,6 +12576,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + @@ -13049,1351 +12830,6 @@ binary, and takes no temporal argument. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/ro-full.json b/ro-full.json index 3d4c0d6e..10cabfc6 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" : "2024-02-13" + "val" : "2024-04-24" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro-full.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-04-24/ro-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -2291,6 +2291,40 @@ "val" : "EL++ ontology module" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000011", + "lbl" : "planned process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that realizes a plan which is the concretization of a plan specification." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Injecting mice with a vaccine in order to test its efficacy" + }, { + "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" : "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "branch derived" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000047", "lbl" : "processed material", @@ -2313,6 +2347,40 @@ "val" : "PERSON: Alan Ruttenberg" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000070", + "lbl" : "assay", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "assay" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house." + }, { + "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" : "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PlanAndPlannedProcess Branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "measuring" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "scientific observation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI branch derived" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000967", "lbl" : "container", @@ -2649,6 +2717,33 @@ "xrefs" : [ "ISBN:0881923214" ] } } + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0001470", + "lbl" : "proportionality to", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity.", + "xrefs" : [ "PATOC:nw" ] + }, + "comments" : [ "Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "proportion" + }, { + "pred" : "hasExactSynonym", + "val" : "proportionality" + }, { + "pred" : "hasExactSynonym", + "val" : "quotient" + }, { + "pred" : "hasExactSynonym", + "val" : "ratio" + }, { + "pred" : "hasRelatedSynonym", + "val" : "rate" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002124", "lbl" : "laminar", @@ -2721,9 +2816,6 @@ }, { "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" } ] } }, { @@ -5756,11 +5848,11 @@ "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" } ] } }, { @@ -8316,6 +8408,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -8340,6 +8435,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -8576,6 +8674,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -8736,6 +8837,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -8747,6 +8851,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -8761,6 +8868,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -10103,6 +10213,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -10114,6 +10227,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -12318,6 +12434,41 @@ "val" : "https://orcid.org/0000-0002-8844-9165" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009006", + "lbl" : "assay measures characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8844-9165" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-05-23T15:24:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009007", + "lbl" : "characteristic measured by assay", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'assay measures characteristic'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8844-9165" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-05-23T15:29:50Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -13322,18 +13473,18 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" @@ -13390,6 +13541,82 @@ "val" : "https://orcid.org/0000-0002-5714-991X" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017006", + "lbl" : "has maximum capacity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube has maximum capacity 10 ml." + }, { + "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_0017008", + "lbl" : "owns", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A primitive relation that holds between entities x and y in which y is at x's full disposal." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "biobank organization owns a specimen" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "hospital owns a laboratory facility" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1834-3856" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-03-29T16:57:03Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017009", + "lbl" : "is owned by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of the owns relation." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "freezer is owned by a biobank organization" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1834-3856" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-03-29T17:06:06Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -13858,6 +14085,40 @@ "val" : "2024-02-01T10:09:59Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -16361,6 +16622,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0001-8314-2140", + "lbl" : "Raymund Stefancsik", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0001-8910-9851", "lbl" : "Lynn Schriml", @@ -16371,6 +16642,16 @@ "val" : "researcher, metadata, diseases, University of Maryland" } ] } + }, { + "id" : "https://orcid.org/0000-0001-9625-1899", + "lbl" : "William D Duncan", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-2908-3327", "lbl" : "Anne Thessen", @@ -16461,6 +16742,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-8844-9165", + "lbl" : "Damion M Dooley", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-8844-9165)" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1617-8244", "lbl" : "Lindsay G Cowell", @@ -16481,6 +16772,16 @@ "val" : "Canadian biocurator" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1834-3856", + "lbl" : "Mathias Brochhausen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1909-9269", "lbl" : "S. Clint Dowland", @@ -16501,6 +16802,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-2620-0345", + "lbl" : "Asiyah Yu Lin", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-2620-0345" + } ] + } }, { "id" : "https://orcid.org/0000-0003-3138-4118", "lbl" : "Jorrit Poelen", @@ -16614,10 +16925,6 @@ "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", @@ -16630,10 +16937,18 @@ "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_0000011", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "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_0000070", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000967", "pred" : "is_a", @@ -16662,6 +16977,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001199", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001470", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002124", "pred" : "is_a", @@ -17989,7 +18308,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -18033,15 +18352,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002472", "pred" : "subPropertyOf", @@ -19218,6 +19537,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -19946,6 +20273,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008507", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008508" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0009006", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0009007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0010001", "pred" : "inverseOf", @@ -19970,6 +20301,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0015001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0015002" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0017008", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0017009" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0018002", "pred" : "inverseOf", @@ -19997,10 +20332,6 @@ "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", @@ -20040,13 +20371,6 @@ "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" ], @@ -20065,7 +20389,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", @@ -20073,7 +20397,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", @@ -20475,6 +20799,14 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0009004", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009006", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000070" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009007", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000070" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -20555,6 +20887,10 @@ "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_0017006", + "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" ], @@ -20571,6 +20907,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 5d3d9956..e9baa7f7 100644 --- a/ro-full.obo +++ b/ro-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: ro/releases/2024-02-13/ro-full.owl +data-version: ro/releases/2024-04-24/ro-full.owl subsetdef: common_anatomy "" subsetdef: efo_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" @@ -18,7 +18,7 @@ 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 "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-24" xsd:string [Term] id: BFO:0000002 @@ -57,7 +57,6 @@ 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] @@ -90,7 +89,6 @@ comment: A continuant that inheres in or is borne by other entities. Every insta is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically 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 @@ -384,7 +382,7 @@ 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 +disjoint_from: OBI:0000011 ! planned process created_by: jl creation_date: 2012-09-19T15:05:24Z @@ -423,6 +421,20 @@ 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:0000011 +name: planned process +def: "A process that realizes a plan which is the concretization of a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string +property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000119 "branch derived" xsd:string + [Term] id: OBI:0000047 name: processed material @@ -433,6 +445,20 @@ property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafi property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +[Term] +id: OBI:0000070 +name: assay +def: "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." [] +is_a: OBI:0000011 ! planned process +property_value: IAO:0000111 "assay" xsd:string +property_value: IAO:0000112 "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation." xsd:string +property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string +property_value: IAO:0000118 "measuring" xsd:string +property_value: IAO:0000118 "scientific observation" xsd:string +property_value: IAO:0000119 "OBI branch derived" xsd:string + [Term] id: OBI:0000967 name: container @@ -500,6 +526,18 @@ name: linear def: "A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel." [ISBN:0881923214] is_a: PATO:0000001 ! quality +[Term] +id: PATO:0001470 +name: proportionality to +def: "A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity." [PATOC:nw] +comment: Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right. +synonym: "proportion" EXACT [] +synonym: "proportionality" EXACT [] +synonym: "quotient" EXACT [] +synonym: "rate" RELATED [] +synonym: "ratio" EXACT [] +is_a: PATO:0000001 ! quality + [Term] id: PATO:0002124 name: laminar @@ -888,7 +926,6 @@ 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 @@ -932,7 +969,6 @@ 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 ! characteristic is_inverse_functional: true @@ -961,7 +997,6 @@ 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 @@ -2537,7 +2572,7 @@ is_a: RO:0002444 ! parasite of id: RO:0002238 name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: RO:0000057 ! has participant @@ -3917,6 +3952,7 @@ is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002444 name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string @@ -3930,6 +3966,7 @@ inverse_of: RO:0002445 ! parasitized by [Typedef] id: RO:0002445 name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4053,10 +4090,11 @@ is_a: RO:0002442 ! mutualistically interacts with [Typedef] id: RO:0002457 name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with inverse_of: RO:0002469 ! provides nutrients for [Typedef] @@ -4143,26 +4181,29 @@ is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002469 name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002470 name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002471 name: is eaten by +def: "Inverse of eats" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002472 @@ -4758,6 +4799,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002556 name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002454 ! has host @@ -4766,6 +4808,7 @@ inverse_of: RO:0002557 ! has pathogen [Typedef] id: RO:0002557 name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002453 ! host of @@ -5929,6 +5972,26 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 is_a: RO:0009001 ! has substance added +[Typedef] +id: RO:0009006 +name: assay measures characteristic +def: "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 +property_value: http://purl.org/dc/terms/date "2023-05-23T15:24:15Z" xsd:dateTime +property_value: IAO:0000112 "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material." xsd:string +domain: OBI:0000070 ! assay +range: BFO:0000020 ! characteristic +inverse_of: RO:0009007 ! characteristic measured by assay + +[Typedef] +id: RO:0009007 +name: characteristic measured by assay +def: "Inverse of 'assay measures characteristic'" [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 +property_value: http://purl.org/dc/terms/date "2023-05-23T15:29:50Z" xsd:dateTime +domain: BFO:0000020 ! characteristic +range: OBI:0000070 ! assay + [Typedef] id: RO:0009501 name: realized in response to @@ -6479,9 +6542,9 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: RO:0002215 RO:0002233 @@ -6515,6 +6578,40 @@ property_value: IAO:0000112 "anticoagulant-containing test tube contains measure domain: OBI:0000967 ! container range: COB:0000121 ! measurement datum +[Typedef] +id: RO:0017006 +name: has maximum capacity +def: "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." [] +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 has maximum capacity 10 ml." xsd:string +domain: OBI:0000967 ! container +range: COB:0000121 ! measurement datum + +[Typedef] +id: RO:0017008 +name: owns +def: "A primitive relation that holds between entities x and y in which y is at x's full disposal." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1834-3856 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: http://purl.org/dc/terms/description "This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal." xsd:string +property_value: IAO:0000112 "biobank organization owns a specimen" xsd:string +property_value: IAO:0000112 "hospital owns a laboratory facility" xsd:string +inverse_of: RO:0017009 ! is owned by +creation_date: 2023-03-29T16:57:03Z + +[Typedef] +id: RO:0017009 +name: is owned by +def: "Inverse of the owns relation." [] +subset: RO:0002259 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1834-3856 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: IAO:0000112 "freezer is owned by a biobank organization" xsd:string +creation_date: 2023-03-29T17:06:06Z + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -6753,6 +6850,26 @@ range: UBERON:0000061 ! anatomical structure is_a: RO:0002178 ! supplies is_a: RO:0002179 ! drains +[Typedef] +id: RO:0020202 +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 ! proportionality to +range: PATO:0000001 ! quality +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0020203 +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 ! proportionality to +range: PATO:0000001 ! quality +is_a: BFO:0000051 ! has part + [Typedef] id: RO:0040035 name: disease relationship diff --git a/ro-full.owl b/ro-full.owl index 8f426451..e42245a9 100644 --- a/ro-full.owl +++ b/ro-full.owl @@ -20,11 +20,11 @@ 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 - 2024-02-13 + 2024-04-24 https://github.com/oborel/obo-relations/ @@ -1531,7 +1531,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - part of part of @@ -1561,7 +1560,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has part has part @@ -1676,7 +1674,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - @@ -1696,7 +1693,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -1755,9 +1751,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - has characteristic has characteristic - https://github.com/oborel/obo-relations/pull/284 @@ -1783,7 +1777,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - @@ -1802,7 +1795,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant has participant @@ -4406,10 +4398,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + has component participant @@ -5287,7 +5279,6 @@ 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 @@ -6570,6 +6561,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes direct parasite of @@ -6585,6 +6577,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -6778,8 +6771,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. @@ -6916,7 +6910,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. provides nutrients for @@ -6927,7 +6922,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with @@ -6939,7 +6935,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -7927,6 +7924,7 @@ the a supports either the existence of b, or the truth value of b. + Inverse of has pathogen pathogen of @@ -7938,6 +7936,7 @@ the a supports either the existence of b, or the truth value of b. + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member has pathogen @@ -9777,6 +9776,34 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material. + A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic. + + 2023-05-23T15:24:15Z + assay measures characteristic + + + + + + + + + + Inverse of 'assay measures characteristic' + + 2023-05-23T15:29:50Z + characteristic measured by assay + + + + @@ -10651,10 +10678,10 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 + + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -10703,6 +10730,52 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + anticoagulant-containing test tube has maximum capacity 10 ml. + A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume. + + + has maximum capacity + + + + + + + + + biobank organization owns a specimen + hospital owns a laboratory facility + A primitive relation that holds between entities x and y in which y is at x's full disposal. + + + + This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal. + 2023-03-29T16:57:03Z + owns + + + + + + + + freezer is owned by a biobank organization + Inverse of the owns relation. + + + + 2023-03-29T17:06:06Z + + is owned by + + + + @@ -11119,6 +11192,34 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + A relationship between a ratio or proportion and its dividend. + + has dividend + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + has divisor + has denominator + + + + @@ -12905,12 +13006,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - - - - - - @@ -12977,12 +13072,6 @@ 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. @@ -14199,12 +14288,7 @@ 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 @@ -14345,6 +14429,25 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A process that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + planned process + + + + @@ -14359,6 +14462,24 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + assay + Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. + + A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. + 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. + PlanAndPlannedProcess Branch + measuring + scientific observation + OBI branch derived + assay + + + + @@ -14487,6 +14608,29 @@ This issue is outside the scope of OBI. + + + + + A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity. + proportion + proportionality + quotient + ratio + rate + PATO:0001470 + Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right. + proportionality to + + + + + A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity. + PATOC:nw + + + + @@ -15173,6 +15317,27 @@ binary, and takes no temporal argument. + + + + researcher + Raymund Stefancsik + + + + + researcher + + + + + + Raymund Stefancsik + + + + + @@ -15194,6 +15359,27 @@ binary, and takes no temporal argument. + + + + researcher + William D Duncan + + + + + researcher + + + + + + William D Duncan + + + + + @@ -15383,6 +15569,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-8844-9165) + Damion M Dooley + + + + + researcher (ORCID 0000-0002-8844-9165) + + + + + + Damion M Dooley + + + + + @@ -15425,6 +15632,27 @@ binary, and takes no temporal argument. + + + + researcher + Mathias Brochhausen + + + + + researcher + + + + + + Mathias Brochhausen + + + + + @@ -15467,6 +15695,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0003-2620-0345 + Asiyah Yu Lin + + + + + Researcher ORCID=0000-0003-2620-0345 + + + + + + Asiyah Yu Lin + + + + + @@ -16050,15 +16299,15 @@ No imports - - - + + + @@ -16738,9 +16987,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16749,9 +16998,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16783,9 +17032,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16794,9 +17043,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16828,9 +17077,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16839,9 +17088,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16873,9 +17122,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16884,9 +17133,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16918,9 +17167,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16929,9 +17178,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16963,7 +17212,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16974,7 +17223,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16991,7 +17240,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17001,7 +17250,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17019,7 +17268,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17030,7 +17279,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17047,7 +17296,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17057,7 +17306,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17074,7 +17323,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17085,7 +17334,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17118,9 +17367,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17129,9 +17378,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17162,9 +17411,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17173,9 +17422,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17206,9 +17455,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17217,9 +17466,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17250,9 +17499,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17261,9 +17510,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17295,8 +17544,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -17306,8 +17555,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + diff --git a/ro.json b/ro.json index 447a2acb..947e48d9 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" : "2024-02-13" + "val" : "2024-04-24" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-04-24/ro.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -2291,6 +2291,40 @@ "val" : "EL++ ontology module" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000011", + "lbl" : "planned process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that realizes a plan which is the concretization of a plan specification." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Injecting mice with a vaccine in order to test its efficacy" + }, { + "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" : "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "branch derived" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000047", "lbl" : "processed material", @@ -2313,6 +2347,40 @@ "val" : "PERSON: Alan Ruttenberg" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000070", + "lbl" : "assay", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "assay" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house." + }, { + "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" : "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PlanAndPlannedProcess Branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "measuring" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "scientific observation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI branch derived" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000967", "lbl" : "container", @@ -2649,6 +2717,33 @@ "xrefs" : [ "ISBN:0881923214" ] } } + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0001470", + "lbl" : "proportionality to", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity.", + "xrefs" : [ "PATOC:nw" ] + }, + "comments" : [ "Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "proportion" + }, { + "pred" : "hasExactSynonym", + "val" : "proportionality" + }, { + "pred" : "hasExactSynonym", + "val" : "quotient" + }, { + "pred" : "hasExactSynonym", + "val" : "ratio" + }, { + "pred" : "hasRelatedSynonym", + "val" : "rate" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002124", "lbl" : "laminar", @@ -2721,9 +2816,6 @@ }, { "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" } ] } }, { @@ -5756,11 +5848,11 @@ "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" } ] } }, { @@ -8316,6 +8408,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -8340,6 +8435,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -8576,6 +8674,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -8736,6 +8837,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -8747,6 +8851,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -8761,6 +8868,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -10103,6 +10213,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -10114,6 +10227,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -12318,6 +12434,41 @@ "val" : "https://orcid.org/0000-0002-8844-9165" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009006", + "lbl" : "assay measures characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8844-9165" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-05-23T15:24:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009007", + "lbl" : "characteristic measured by assay", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'assay measures characteristic'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8844-9165" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-05-23T15:29:50Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -13322,18 +13473,18 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" @@ -13390,6 +13541,82 @@ "val" : "https://orcid.org/0000-0002-5714-991X" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017006", + "lbl" : "has maximum capacity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube has maximum capacity 10 ml." + }, { + "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_0017008", + "lbl" : "owns", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A primitive relation that holds between entities x and y in which y is at x's full disposal." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "biobank organization owns a specimen" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "hospital owns a laboratory facility" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1834-3856" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-03-29T16:57:03Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017009", + "lbl" : "is owned by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of the owns relation." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "freezer is owned by a biobank organization" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1834-3856" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-03-29T17:06:06Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -13858,6 +14085,40 @@ "val" : "2024-02-01T10:09:59Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -16361,6 +16622,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0001-8314-2140", + "lbl" : "Raymund Stefancsik", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0001-8910-9851", "lbl" : "Lynn Schriml", @@ -16371,6 +16642,16 @@ "val" : "researcher, metadata, diseases, University of Maryland" } ] } + }, { + "id" : "https://orcid.org/0000-0001-9625-1899", + "lbl" : "William D Duncan", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-2908-3327", "lbl" : "Anne Thessen", @@ -16461,6 +16742,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-8844-9165", + "lbl" : "Damion M Dooley", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-8844-9165)" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1617-8244", "lbl" : "Lindsay G Cowell", @@ -16481,6 +16772,16 @@ "val" : "Canadian biocurator" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1834-3856", + "lbl" : "Mathias Brochhausen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1909-9269", "lbl" : "S. Clint Dowland", @@ -16501,6 +16802,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-2620-0345", + "lbl" : "Asiyah Yu Lin", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-2620-0345" + } ] + } }, { "id" : "https://orcid.org/0000-0003-3138-4118", "lbl" : "Jorrit Poelen", @@ -16614,10 +16925,6 @@ "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", @@ -16630,10 +16937,18 @@ "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_0000011", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "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_0000070", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000967", "pred" : "is_a", @@ -16662,6 +16977,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001199", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001470", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002124", "pred" : "is_a", @@ -17989,7 +18308,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -18033,15 +18352,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002472", "pred" : "subPropertyOf", @@ -19218,6 +19537,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -19946,6 +20273,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008507", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008508" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0009006", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0009007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0010001", "pred" : "inverseOf", @@ -19970,6 +20301,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0015001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0015002" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0017008", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0017009" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0018002", "pred" : "inverseOf", @@ -19997,10 +20332,6 @@ "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", @@ -20040,13 +20371,6 @@ "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" ], @@ -20065,7 +20389,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", @@ -20073,7 +20397,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", @@ -20475,6 +20799,14 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0009004", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009006", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000070" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009007", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000070" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -20555,6 +20887,10 @@ "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_0017006", + "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" ], @@ -20571,6 +20907,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 29ad9099..edef8a1c 100644 --- a/ro.obo +++ b/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2024-02-13 +data-version: releases/2024-04-24 subsetdef: common_anatomy "" subsetdef: efo_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" @@ -18,7 +18,7 @@ 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 "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-24" xsd:string [Term] id: BFO:0000002 @@ -57,7 +57,6 @@ 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] @@ -90,7 +89,6 @@ comment: A continuant that inheres in or is borne by other entities. Every insta is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically 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 @@ -384,7 +382,7 @@ 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 +disjoint_from: OBI:0000011 ! planned process created_by: jl creation_date: 2012-09-19T15:05:24Z @@ -423,6 +421,20 @@ 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:0000011 +name: planned process +def: "A process that realizes a plan which is the concretization of a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string +property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000119 "branch derived" xsd:string + [Term] id: OBI:0000047 name: processed material @@ -433,6 +445,20 @@ property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafi property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +[Term] +id: OBI:0000070 +name: assay +def: "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." [] +is_a: OBI:0000011 ! planned process +property_value: IAO:0000111 "assay" xsd:string +property_value: IAO:0000112 "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation." xsd:string +property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string +property_value: IAO:0000118 "measuring" xsd:string +property_value: IAO:0000118 "scientific observation" xsd:string +property_value: IAO:0000119 "OBI branch derived" xsd:string + [Term] id: OBI:0000967 name: container @@ -500,6 +526,18 @@ name: linear def: "A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel." [ISBN:0881923214] is_a: PATO:0000001 ! quality +[Term] +id: PATO:0001470 +name: proportionality to +def: "A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity." [PATOC:nw] +comment: Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right. +synonym: "proportion" EXACT [] +synonym: "proportionality" EXACT [] +synonym: "quotient" EXACT [] +synonym: "rate" RELATED [] +synonym: "ratio" EXACT [] +is_a: PATO:0000001 ! quality + [Term] id: PATO:0002124 name: laminar @@ -888,7 +926,6 @@ 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 @@ -932,7 +969,6 @@ 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 ! characteristic is_inverse_functional: true @@ -961,7 +997,6 @@ 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 @@ -2537,7 +2572,7 @@ is_a: RO:0002444 ! parasite of id: RO:0002238 name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: RO:0000057 ! has participant @@ -3917,6 +3952,7 @@ is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002444 name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string @@ -3930,6 +3966,7 @@ inverse_of: RO:0002445 ! parasitized by [Typedef] id: RO:0002445 name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4053,10 +4090,11 @@ is_a: RO:0002442 ! mutualistically interacts with [Typedef] id: RO:0002457 name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with inverse_of: RO:0002469 ! provides nutrients for [Typedef] @@ -4143,26 +4181,29 @@ is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002469 name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002470 name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002471 name: is eaten by +def: "Inverse of eats" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002472 @@ -4758,6 +4799,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002556 name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002454 ! has host @@ -4766,6 +4808,7 @@ inverse_of: RO:0002557 ! has pathogen [Typedef] id: RO:0002557 name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002453 ! host of @@ -5929,6 +5972,26 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 is_a: RO:0009001 ! has substance added +[Typedef] +id: RO:0009006 +name: assay measures characteristic +def: "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 +property_value: http://purl.org/dc/terms/date "2023-05-23T15:24:15Z" xsd:dateTime +property_value: IAO:0000112 "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material." xsd:string +domain: OBI:0000070 ! assay +range: BFO:0000020 ! characteristic +inverse_of: RO:0009007 ! characteristic measured by assay + +[Typedef] +id: RO:0009007 +name: characteristic measured by assay +def: "Inverse of 'assay measures characteristic'" [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 +property_value: http://purl.org/dc/terms/date "2023-05-23T15:29:50Z" xsd:dateTime +domain: BFO:0000020 ! characteristic +range: OBI:0000070 ! assay + [Typedef] id: RO:0009501 name: realized in response to @@ -6479,9 +6542,9 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: RO:0002215 RO:0002233 @@ -6515,6 +6578,40 @@ property_value: IAO:0000112 "anticoagulant-containing test tube contains measure domain: OBI:0000967 ! container range: COB:0000121 ! measurement datum +[Typedef] +id: RO:0017006 +name: has maximum capacity +def: "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." [] +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 has maximum capacity 10 ml." xsd:string +domain: OBI:0000967 ! container +range: COB:0000121 ! measurement datum + +[Typedef] +id: RO:0017008 +name: owns +def: "A primitive relation that holds between entities x and y in which y is at x's full disposal." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1834-3856 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: http://purl.org/dc/terms/description "This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal." xsd:string +property_value: IAO:0000112 "biobank organization owns a specimen" xsd:string +property_value: IAO:0000112 "hospital owns a laboratory facility" xsd:string +inverse_of: RO:0017009 ! is owned by +creation_date: 2023-03-29T16:57:03Z + +[Typedef] +id: RO:0017009 +name: is owned by +def: "Inverse of the owns relation." [] +subset: RO:0002259 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1834-3856 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 +property_value: IAO:0000112 "freezer is owned by a biobank organization" xsd:string +creation_date: 2023-03-29T17:06:06Z + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -6753,6 +6850,26 @@ range: UBERON:0000061 ! anatomical structure is_a: RO:0002178 ! supplies is_a: RO:0002179 ! drains +[Typedef] +id: RO:0020202 +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 ! proportionality to +range: PATO:0000001 ! quality +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0020203 +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 ! proportionality to +range: PATO:0000001 ! quality +is_a: BFO:0000051 ! has part + [Typedef] id: RO:0040035 name: disease relationship diff --git a/ro.owl b/ro.owl index 8f5e4eb0..f8f35a10 100644 --- a/ro.owl +++ b/ro.owl @@ -20,11 +20,11 @@ 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 - 2024-02-13 + 2024-04-24 https://github.com/oborel/obo-relations/ @@ -1531,7 +1531,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - part of part of @@ -1561,7 +1560,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has part has part @@ -1676,7 +1674,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - @@ -1696,7 +1693,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -1755,9 +1751,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - has characteristic has characteristic - https://github.com/oborel/obo-relations/pull/284 @@ -1783,7 +1777,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - @@ -1802,7 +1795,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant has participant @@ -4406,10 +4398,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + has component participant @@ -5287,7 +5279,6 @@ 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 @@ -6570,6 +6561,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes direct parasite of @@ -6585,6 +6577,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -6778,8 +6771,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. @@ -6916,7 +6910,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. provides nutrients for @@ -6927,7 +6922,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with @@ -6939,7 +6935,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -7927,6 +7924,7 @@ the a supports either the existence of b, or the truth value of b. + Inverse of has pathogen pathogen of @@ -7938,6 +7936,7 @@ the a supports either the existence of b, or the truth value of b. + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member has pathogen @@ -9777,6 +9776,34 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material. + A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic. + + 2023-05-23T15:24:15Z + assay measures characteristic + + + + + + + + + + Inverse of 'assay measures characteristic' + + 2023-05-23T15:29:50Z + characteristic measured by assay + + + + @@ -10651,10 +10678,10 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 + + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -10703,6 +10730,52 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + anticoagulant-containing test tube has maximum capacity 10 ml. + A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume. + + + has maximum capacity + + + + + + + + + biobank organization owns a specimen + hospital owns a laboratory facility + A primitive relation that holds between entities x and y in which y is at x's full disposal. + + + + This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal. + 2023-03-29T16:57:03Z + owns + + + + + + + + freezer is owned by a biobank organization + Inverse of the owns relation. + + + + 2023-03-29T17:06:06Z + + is owned by + + + + @@ -11119,6 +11192,34 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + A relationship between a ratio or proportion and its dividend. + + has dividend + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + has divisor + has denominator + + + + @@ -12905,12 +13006,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - - - - - - @@ -12977,12 +13072,6 @@ 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. @@ -14199,12 +14288,7 @@ 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 @@ -14345,6 +14429,25 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A process that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + planned process + + + + @@ -14359,6 +14462,24 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + assay + Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. + + A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. + 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. + PlanAndPlannedProcess Branch + measuring + scientific observation + OBI branch derived + assay + + + + @@ -14487,6 +14608,29 @@ This issue is outside the scope of OBI. + + + + + A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity. + proportion + proportionality + quotient + ratio + rate + PATO:0001470 + Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right. + proportionality to + + + + + A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity. + PATOC:nw + + + + @@ -15173,6 +15317,27 @@ binary, and takes no temporal argument. + + + + researcher + Raymund Stefancsik + + + + + researcher + + + + + + Raymund Stefancsik + + + + + @@ -15194,6 +15359,27 @@ binary, and takes no temporal argument. + + + + researcher + William D Duncan + + + + + researcher + + + + + + William D Duncan + + + + + @@ -15383,6 +15569,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-8844-9165) + Damion M Dooley + + + + + researcher (ORCID 0000-0002-8844-9165) + + + + + + Damion M Dooley + + + + + @@ -15425,6 +15632,27 @@ binary, and takes no temporal argument. + + + + researcher + Mathias Brochhausen + + + + + researcher + + + + + + Mathias Brochhausen + + + + + @@ -15467,6 +15695,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0003-2620-0345 + Asiyah Yu Lin + + + + + Researcher ORCID=0000-0003-2620-0345 + + + + + + Asiyah Yu Lin + + + + + @@ -16053,15 +16302,15 @@ No imports - - - + + + @@ -16740,9 +16989,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16751,9 +17000,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16785,9 +17034,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16796,9 +17045,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16830,9 +17079,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16841,9 +17090,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16875,9 +17124,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16886,9 +17135,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16920,9 +17169,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16931,9 +17180,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -16965,7 +17214,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16976,7 +17225,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16993,7 +17242,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17003,7 +17252,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17021,7 +17270,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17032,7 +17281,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17049,7 +17298,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17059,7 +17308,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17076,7 +17325,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17087,7 +17336,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -17120,9 +17369,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17131,9 +17380,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17164,9 +17413,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17175,9 +17424,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17208,9 +17457,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17219,9 +17468,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17252,9 +17501,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17263,9 +17512,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17297,8 +17546,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -17308,8 +17557,8 @@ 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 507a3345..6870be9e 100644 --- a/src/ontology/imports/orcidio_import.owl +++ b/src/ontology/imports/orcidio_import.owl @@ -7,12 +7,13 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-02-12") + +Annotation(owl:versionInfo "2024-04-04") Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -24,12 +25,13 @@ 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()) @@ -58,6 +60,11 @@ AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Shawn Zheng Kai Tan") +# Individual: (Raymund Stefancsik) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "Raymund Stefancsik") + # Individual: (Lynn Schriml) AnnotationAssertion(Annotation( ) "researcher, metadata, diseases, University of Maryland") @@ -113,6 +120,11 @@ AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "James P. Balhoff") +# Individual: (Damion M Dooley) + +AnnotationAssertion(Annotation( ) "researcher (ORCID 0000-0002-8844-9165)") +AnnotationAssertion(Annotation( ) rdfs:label "Damion M Dooley") + # Individual: (Lindsay G Cowell) AnnotationAssertion(Annotation( ) "researcher") @@ -123,11 +135,11 @@ AnnotationAssertion(Annotation( ) "Canadian biocurator") AnnotationAssertion(Annotation( ) rdfs:label "Pascale Gaudet") - # Individual: (Mathias Brochhausen) AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Mathias Brochhausen") + # Individual: (S. Clint Dowland) AnnotationAssertion(Annotation( ) "Researcher ORCID=0000-0003-1909-9269") @@ -138,6 +150,11 @@ AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Anna Maria Masci") +# Individual: (Asiyah Yu Lin) + +AnnotationAssertion(Annotation( ) "Researcher ORCID=0000-0003-2620-0345") +AnnotationAssertion(Annotation( ) rdfs:label "Asiyah Yu Lin") + # Individual: (Jorrit Poelen) AnnotationAssertion(Annotation( ) "software/data engineer") diff --git a/src/ontology/subsets/ro-biotic-interaction.json b/src/ontology/subsets/ro-biotic-interaction.json index 9fd62d8e..00fa6c6c 100644 --- a/src/ontology/subsets/ro-biotic-interaction.json +++ b/src/ontology/subsets/ro-biotic-interaction.json @@ -222,6 +222,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -246,6 +249,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -368,6 +374,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -436,6 +445,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -447,6 +459,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -461,6 +476,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -552,6 +570,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -563,6 +584,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -929,7 +953,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -945,15 +969,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002553", "pred" : "subPropertyOf", diff --git a/src/ontology/subsets/ro-biotic-interaction.obo b/src/ontology/subsets/ro-biotic-interaction.obo index 82eed56a..47c649b9 100644 --- a/src/ontology/subsets/ro-biotic-interaction.obo +++ b/src/ontology/subsets/ro-biotic-interaction.obo @@ -124,6 +124,7 @@ is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002444 name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string @@ -137,6 +138,7 @@ inverse_of: RO:0002445 ! parasitized by [Typedef] id: RO:0002445 name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -199,10 +201,11 @@ is_a: RO:0002442 ! mutualistically interacts with [Typedef] id: RO:0002457 name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with inverse_of: RO:0002469 ! provides nutrients for [Typedef] @@ -238,26 +241,29 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002469 name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002470 name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002471 name: is eaten by +def: "Inverse of eats" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002553 @@ -300,6 +306,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002556 name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002454 ! has host @@ -308,6 +315,7 @@ inverse_of: RO:0002557 ! has pathogen [Typedef] id: RO:0002557 name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002453 ! host of diff --git a/src/ontology/subsets/ro-biotic-interaction.owl b/src/ontology/subsets/ro-biotic-interaction.owl index 2373adf8..d7993f48 100644 --- a/src/ontology/subsets/ro-biotic-interaction.owl +++ b/src/ontology/subsets/ro-biotic-interaction.owl @@ -290,6 +290,7 @@ Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes direct parasite of @@ -305,6 +306,7 @@ + Inverse of parasite of has parasite parasitised by @@ -389,8 +391,9 @@ - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. @@ -444,7 +447,8 @@ - + + A biotic interaction where a material entity provides nutrition for an organism. provides nutrients for @@ -455,7 +459,8 @@ - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with @@ -467,7 +472,8 @@ - + + Inverse of eats eaten by is target of eating interaction with @@ -538,6 +544,7 @@ + Inverse of has pathogen pathogen of @@ -549,6 +556,7 @@ + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member has pathogen diff --git a/src/ontology/subsets/ro-causal.json b/src/ontology/subsets/ro-causal.json index 995c9dab..d3ae1433 100644 --- a/src/ontology/subsets/ro-causal.json +++ b/src/ontology/subsets/ro-causal.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 b2bf3775..f4dea7b7 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index 5284eca2..06869f0a 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ 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 958994a5..6450b98d 100644 --- a/src/ontology/subsets/ro-causal.tsv +++ b/src/ontology/subsets/ro-causal.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid1 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid18 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid22 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid26 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid33 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid37 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid40 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid5 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid52 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid58 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid61 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid64 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid67 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid9 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid1 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid18 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid22 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid26 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid33 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid37 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid40 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid5 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid52 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid58 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid61 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid64 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid67 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid9 @@ -39,6 +39,7 @@ _:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid9 + diff --git a/src/ontology/subsets/ro-chado.json b/src/ontology/subsets/ro-chado.json index 492b6f02..42a369a4 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" : "2024-02-13" + "val" : "2024-04-24" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/subsets/ro-chado.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-04-24/subsets/ro-chado.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -1838,9 +1838,6 @@ }, { "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" } ] } }, { @@ -4873,11 +4870,11 @@ "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" } ] } }, { @@ -7401,6 +7398,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -7425,6 +7425,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -7661,6 +7664,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -7821,6 +7827,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -7832,6 +7841,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -7846,6 +7858,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -9143,6 +9158,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -9154,6 +9172,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11339,6 +11360,41 @@ "val" : "https://orcid.org/0000-0002-8844-9165" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009006", + "lbl" : "assay measures characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8844-9165" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-05-23T15:24:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009007", + "lbl" : "characteristic measured by assay", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'assay measures characteristic'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8844-9165" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-05-23T15:29:50Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -12343,18 +12399,18 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" @@ -12411,6 +12467,82 @@ "val" : "https://orcid.org/0000-0002-5714-991X" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017006", + "lbl" : "has maximum capacity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube has maximum capacity 10 ml." + }, { + "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_0017008", + "lbl" : "owns", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A primitive relation that holds between entities x and y in which y is at x's full disposal." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "biobank organization owns a specimen" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "hospital owns a laboratory facility" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1834-3856" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-03-29T16:57:03Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017009", + "lbl" : "is owned by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of the owns relation." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "freezer is owned by a biobank organization" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1834-3856" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-03-29T17:06:06Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -12879,6 +13011,40 @@ "val" : "2024-02-01T10:09:59Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -14988,6 +15154,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0001-8314-2140", + "lbl" : "Raymund Stefancsik", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0001-8910-9851", "lbl" : "Lynn Schriml", @@ -14998,6 +15174,16 @@ "val" : "researcher, metadata, diseases, University of Maryland" } ] } + }, { + "id" : "https://orcid.org/0000-0001-9625-1899", + "lbl" : "William D Duncan", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-2908-3327", "lbl" : "Anne Thessen", @@ -15088,6 +15274,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-8844-9165", + "lbl" : "Damion M Dooley", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-8844-9165)" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1617-8244", "lbl" : "Lindsay G Cowell", @@ -15108,6 +15304,16 @@ "val" : "Canadian biocurator" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1834-3856", + "lbl" : "Mathias Brochhausen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1909-9269", "lbl" : "S. Clint Dowland", @@ -15128,6 +15334,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-2620-0345", + "lbl" : "Asiyah Yu Lin", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-2620-0345" + } ] + } }, { "id" : "https://orcid.org/0000-0003-3138-4118", "lbl" : "Jorrit Poelen", @@ -16404,7 +16620,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -16448,15 +16664,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002472", "pred" : "subPropertyOf", @@ -17625,6 +17841,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -18353,6 +18577,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008507", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008508" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0009006", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0009007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0010001", "pred" : "inverseOf", @@ -18377,6 +18605,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0015001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0015002" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0017008", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0017009" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0018002", "pred" : "inverseOf", diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index dd45dd89..06a83569 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -18,7 +18,7 @@ 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 "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-24" xsd:string [Typedef] id: BFO:0000050 @@ -1929,6 +1929,7 @@ is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002444 name: parasite_of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] synonym: "direct parasite of" EXACT [] is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002454 ! has host @@ -1937,6 +1938,7 @@ inverse_of: RO:0002445 ! parasitized by [Typedef] id: RO:0002445 name: parasitized_by +def: "Inverse of parasite of" [] synonym: "directly parasitized by" EXACT [] is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002453 ! host of @@ -2012,7 +2014,8 @@ is_a: RO:0002442 ! mutualistically interacts with [Typedef] id: RO:0002457 name: acquires_nutrients_from -is_a: RO:0002438 ! trophically interacts with +def: "Inverse of provides nutrients for" [] +is_a: RO:0002437 ! biotically interacts with inverse_of: RO:0002469 ! provides nutrients for [Typedef] @@ -2074,17 +2077,20 @@ is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002469 name: provides_nutrients_for -is_a: RO:0002438 ! trophically interacts with +def: "A biotic interaction where a material entity provides nutrition for an organism." [] +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002470 name: eats -is_a: RO:0002438 ! trophically interacts with +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002471 name: is_eaten_by -is_a: RO:0002438 ! trophically interacts with +def: "Inverse of eats" [] +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002472 @@ -2493,12 +2499,14 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002556 name: pathogen_of +def: "Inverse of has pathogen" [] is_a: RO:0002454 ! has host inverse_of: RO:0002557 ! has pathogen [Typedef] id: RO:0002557 name: has_pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] is_a: RO:0002453 ! host of [Typedef] @@ -3323,6 +3331,17 @@ name: has_primary_substance_added def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] is_a: RO:0009001 ! has substance added +[Typedef] +id: RO:0009006 +name: assay_measures_characteristic +def: "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." [] +inverse_of: RO:0009007 ! characteristic measured by assay + +[Typedef] +id: RO:0009007 +name: characteristic_measured_by_assay +def: "Inverse of 'assay measures characteristic'" [] + [Typedef] id: RO:0009501 name: realized_in_response_to @@ -3720,6 +3739,22 @@ 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:0017006 +name: has_maximum_capacity +def: "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." [] + +[Typedef] +id: RO:0017008 +name: owns +def: "A primitive relation that holds between entities x and y in which y is at x's full disposal." [] +inverse_of: RO:0017009 ! is owned by + +[Typedef] +id: RO:0017009 +name: is_owned_by +def: "Inverse of the owns relation." [] + [Typedef] id: RO:0018001 name: is_myristoyltransferase_activity @@ -3878,6 +3913,20 @@ def: "x directly supplies and drains y if and only if x is a capillary, y is an is_a: RO:0002178 ! supplies is_a: RO:0002179 ! drains +[Typedef] +id: RO:0020202 +name: has_numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0020203 +name: has_denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +is_a: BFO:0000051 ! has part + [Typedef] id: RO:0040035 name: disease_relationship diff --git a/src/ontology/subsets/ro-chado.owl b/src/ontology/subsets/ro-chado.owl index 76b4fd58..48dcd16e 100644 --- a/src/ontology/subsets/ro-chado.owl +++ b/src/ontology/subsets/ro-chado.owl @@ -20,8 +20,8 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2024-02-13 + + 2024-04-24 @@ -1527,7 +1527,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - part of part of @@ -1557,7 +1556,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has part has part @@ -1681,7 +1679,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -1739,9 +1736,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - has characteristic has characteristic - https://github.com/oborel/obo-relations/pull/284 @@ -1781,7 +1776,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant has participant @@ -4132,10 +4126,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + has component participant @@ -4992,7 +4986,6 @@ 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 @@ -6229,6 +6222,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes direct parasite of @@ -6244,6 +6238,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -6430,8 +6425,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. @@ -6568,7 +6564,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. provides nutrients for @@ -6579,7 +6576,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with @@ -6591,7 +6589,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -7505,6 +7504,7 @@ the a supports either the existence of b, or the truth value of b. + Inverse of has pathogen pathogen of @@ -7516,6 +7516,7 @@ the a supports either the existence of b, or the truth value of b. + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member has pathogen @@ -9257,6 +9258,30 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material. + A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic. + + 2023-05-23T15:24:15Z + assay measures characteristic + + + + + + + + Inverse of 'assay measures characteristic' + + 2023-05-23T15:29:50Z + characteristic measured by assay + + + + @@ -10093,10 +10118,10 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 + + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -10143,6 +10168,50 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + anticoagulant-containing test tube has maximum capacity 10 ml. + A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume. + + + has maximum capacity + + + + + + + + + biobank organization owns a specimen + hospital owns a laboratory facility + A primitive relation that holds between entities x and y in which y is at x's full disposal. + + + + This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal. + 2023-03-29T16:57:03Z + owns + + + + + + + + freezer is owned by a biobank organization + Inverse of the owns relation. + + + + 2023-03-29T17:06:06Z + + is owned by + + + + @@ -10551,6 +10620,30 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + A relationship between a ratio or proportion and its dividend. + + has dividend + has numerator + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + has divisor + has denominator + + + + @@ -12457,6 +12550,27 @@ binary, and takes no temporal argument. + + + + researcher + Raymund Stefancsik + + + + + researcher + + + + + + Raymund Stefancsik + + + + + @@ -12478,6 +12592,27 @@ binary, and takes no temporal argument. + + + + researcher + William D Duncan + + + + + researcher + + + + + + William D Duncan + + + + + @@ -12667,6 +12802,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-8844-9165) + Damion M Dooley + + + + + researcher (ORCID 0000-0002-8844-9165) + + + + + + Damion M Dooley + + + + + @@ -12709,6 +12865,27 @@ binary, and takes no temporal argument. + + + + researcher + Mathias Brochhausen + + + + + researcher + + + + + + Mathias Brochhausen + + + + + @@ -12751,6 +12928,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0003-2620-0345 + Asiyah Yu Lin + + + + + Researcher ORCID=0000-0003-2620-0345 + + + + + + Asiyah Yu Lin + + + + + @@ -13259,15 +13457,15 @@ No imports - - - + + + @@ -13277,15 +13475,15 @@ No imports - - - + + + @@ -13473,9 +13671,9 @@ No imports - - - + + + @@ -13484,9 +13682,9 @@ No imports - - - + + + @@ -13518,9 +13716,9 @@ No imports - + - + @@ -13529,9 +13727,9 @@ No imports - + - + @@ -13563,9 +13761,9 @@ No imports - + - + @@ -13574,9 +13772,9 @@ No imports - + - + @@ -13608,9 +13806,9 @@ No imports - + - + @@ -13619,9 +13817,9 @@ No imports - + - + @@ -13653,9 +13851,9 @@ No imports - + - + @@ -13664,9 +13862,9 @@ No imports - + - + @@ -13697,7 +13895,7 @@ No imports - + @@ -13708,7 +13906,7 @@ No imports - + @@ -13741,9 +13939,9 @@ No imports - - - + + + @@ -13752,9 +13950,9 @@ No imports - - - + + + @@ -13785,9 +13983,9 @@ No imports - - - + + + @@ -13796,9 +13994,9 @@ No imports - - - + + + @@ -13829,9 +14027,9 @@ No imports - - - + + + @@ -13840,9 +14038,9 @@ No imports - - - + + + @@ -13873,9 +14071,9 @@ No imports - - - + + + @@ -13884,9 +14082,9 @@ No imports - - - + + + @@ -13918,8 +14116,8 @@ No imports - - + + @@ -13929,8 +14127,8 @@ No imports - - + + diff --git a/src/ontology/subsets/ro-developmental.json b/src/ontology/subsets/ro-developmental.json index d6d32493..006ef119 100644 --- a/src/ontology/subsets/ro-developmental.json +++ b/src/ontology/subsets/ro-developmental.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 6518ba78..d6bae920 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index 5f2ee16a..0fd9be78 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ 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 3095b994..de55b64b 100644 --- a/src/ontology/subsets/ro-developmental.tsv +++ b/src/ontology/subsets/ro-developmental.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid1 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid18 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid22 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid26 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid33 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid37 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid40 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid5 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid52 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid58 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid61 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid64 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid67 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid9 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid1 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid18 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid22 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid26 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid33 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid37 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid40 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid5 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid52 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid58 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid61 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid64 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid67 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid9 @@ -39,6 +39,7 @@ _:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid9 + diff --git a/src/ontology/subsets/ro-interaction.json b/src/ontology/subsets/ro-interaction.json index 63fc49ba..35526c31 100644 --- a/src/ontology/subsets/ro-interaction.json +++ b/src/ontology/subsets/ro-interaction.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 122c9d98..43c72c85 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index 6c96e01f..bb09791e 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ 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 8318d6a8..0d17032c 100644 --- a/src/ontology/subsets/ro-interaction.tsv +++ b/src/ontology/subsets/ro-interaction.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid1 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid18 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid22 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid26 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid33 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid37 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid40 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid5 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid52 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid58 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid61 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid64 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid67 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid9 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid1 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid18 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid22 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid26 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid33 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid37 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid40 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid5 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid52 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid58 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid61 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid64 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid67 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid9 @@ -39,6 +39,7 @@ _:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid9 + diff --git a/src/ontology/subsets/ro-mereotopology.json b/src/ontology/subsets/ro-mereotopology.json index d0fdda09..6ed77fde 100644 --- a/src/ontology/subsets/ro-mereotopology.json +++ b/src/ontology/subsets/ro-mereotopology.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 31d0bd7e..41ec74b6 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index b0654e52..9938010f 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ 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 87955ff5..082be7e9 100644 --- a/src/ontology/subsets/ro-mereotopology.tsv +++ b/src/ontology/subsets/ro-mereotopology.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid1 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid18 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid22 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid26 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid33 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid37 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid40 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid5 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid52 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid58 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid61 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid64 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid67 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid9 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid1 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid18 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid22 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid26 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid33 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid37 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid40 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid5 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid52 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid58 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid61 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid64 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid67 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid9 @@ -39,6 +39,7 @@ _:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid9 + diff --git a/src/ontology/subsets/ro-sequence.json b/src/ontology/subsets/ro-sequence.json index 2cfc531b..dc34328e 100644 --- a/src/ontology/subsets/ro-sequence.json +++ b/src/ontology/subsets/ro-sequence.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 bbbc3979..542548c2 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index 359bce8a..8355f3bf 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ 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 aabcd030..41d67ec5 100644 --- a/src/ontology/subsets/ro-sequence.tsv +++ b/src/ontology/subsets/ro-sequence.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid1 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid18 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid22 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid26 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid33 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid37 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid40 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid5 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid52 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid58 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid61 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid64 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid67 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid9 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid1 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid18 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid22 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid26 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid33 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid37 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid40 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid5 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid52 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid58 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid61 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid64 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid67 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid9 @@ -39,6 +39,7 @@ _:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid9 + diff --git a/src/ontology/subsets/ro-time-interval.json b/src/ontology/subsets/ro-time-interval.json index 4acf12c3..7c5d6f3f 100644 --- a/src/ontology/subsets/ro-time-interval.json +++ b/src/ontology/subsets/ro-time-interval.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 54ead77f..365558a6 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index a8cde506..7efe6116 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ 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 dadfed7a..a51e190e 100644 --- a/src/ontology/subsets/ro-time-interval.tsv +++ b/src/ontology/subsets/ro-time-interval.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid1 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid18 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid22 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid26 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid33 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid37 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid40 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid5 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid52 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid58 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid61 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid64 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid67 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid9 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid1 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid18 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid22 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid26 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid33 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid37 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid40 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid5 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid52 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid58 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid61 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid64 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid67 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid9 @@ -39,6 +39,7 @@ _:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid9 + diff --git a/subsets/ro-biotic-interaction.json b/subsets/ro-biotic-interaction.json index 9fd62d8e..00fa6c6c 100644 --- a/subsets/ro-biotic-interaction.json +++ b/subsets/ro-biotic-interaction.json @@ -222,6 +222,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -246,6 +249,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -368,6 +374,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -436,6 +445,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -447,6 +459,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -461,6 +476,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -552,6 +570,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -563,6 +584,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -929,7 +953,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -945,15 +969,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002553", "pred" : "subPropertyOf", diff --git a/subsets/ro-biotic-interaction.obo b/subsets/ro-biotic-interaction.obo index 82eed56a..47c649b9 100644 --- a/subsets/ro-biotic-interaction.obo +++ b/subsets/ro-biotic-interaction.obo @@ -124,6 +124,7 @@ is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002444 name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string @@ -137,6 +138,7 @@ inverse_of: RO:0002445 ! parasitized by [Typedef] id: RO:0002445 name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -199,10 +201,11 @@ is_a: RO:0002442 ! mutualistically interacts with [Typedef] id: RO:0002457 name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with inverse_of: RO:0002469 ! provides nutrients for [Typedef] @@ -238,26 +241,29 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002469 name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002470 name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002471 name: is eaten by +def: "Inverse of eats" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002553 @@ -300,6 +306,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002556 name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002454 ! has host @@ -308,6 +315,7 @@ inverse_of: RO:0002557 ! has pathogen [Typedef] id: RO:0002557 name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002453 ! host of diff --git a/subsets/ro-biotic-interaction.owl b/subsets/ro-biotic-interaction.owl index 2373adf8..d7993f48 100644 --- a/subsets/ro-biotic-interaction.owl +++ b/subsets/ro-biotic-interaction.owl @@ -290,6 +290,7 @@ Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes direct parasite of @@ -305,6 +306,7 @@ + Inverse of parasite of has parasite parasitised by @@ -389,8 +391,9 @@ - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. @@ -444,7 +447,8 @@ - + + A biotic interaction where a material entity provides nutrition for an organism. provides nutrients for @@ -455,7 +459,8 @@ - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with @@ -467,7 +472,8 @@ - + + Inverse of eats eaten by is target of eating interaction with @@ -538,6 +544,7 @@ + Inverse of has pathogen pathogen of @@ -549,6 +556,7 @@ + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member has pathogen diff --git a/subsets/ro-causal.json b/subsets/ro-causal.json index 995c9dab..d3ae1433 100644 --- a/subsets/ro-causal.json +++ b/subsets/ro-causal.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 b2bf3775..f4dea7b7 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index 5284eca2..06869f0a 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + diff --git a/subsets/ro-causal.tsv b/subsets/ro-causal.tsv index 958994a5..6450b98d 100644 --- a/subsets/ro-causal.tsv +++ b/subsets/ro-causal.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid1 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid18 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid22 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid26 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid33 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid37 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid40 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid5 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid52 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid58 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid61 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid64 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid67 -_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid9 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid1 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid18 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid22 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid26 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid33 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid37 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid40 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid5 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid52 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid58 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid61 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid64 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid67 +_:B79aafdb5X2Db627X2D4d84X2D9eadX2D80da75dea838genid9 @@ -39,6 +39,7 @@ _:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid9 + diff --git a/subsets/ro-chado.json b/subsets/ro-chado.json index 492b6f02..42a369a4 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" : "2024-02-13" + "val" : "2024-04-24" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/subsets/ro-chado.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-04-24/subsets/ro-chado.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -1838,9 +1838,6 @@ }, { "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" } ] } }, { @@ -4873,11 +4870,11 @@ "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" } ] } }, { @@ -7401,6 +7398,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -7425,6 +7425,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -7661,6 +7664,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -7821,6 +7827,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -7832,6 +7841,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -7846,6 +7858,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -9143,6 +9158,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -9154,6 +9172,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11339,6 +11360,41 @@ "val" : "https://orcid.org/0000-0002-8844-9165" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009006", + "lbl" : "assay measures characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8844-9165" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-05-23T15:24:15Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009007", + "lbl" : "characteristic measured by assay", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'assay measures characteristic'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8844-9165" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-05-23T15:29:50Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", @@ -12343,18 +12399,18 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-2620-0345" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" @@ -12411,6 +12467,82 @@ "val" : "https://orcid.org/0000-0002-5714-991X" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017006", + "lbl" : "has maximum capacity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube has maximum capacity 10 ml." + }, { + "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_0017008", + "lbl" : "owns", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A primitive relation that holds between entities x and y in which y is at x's full disposal." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "biobank organization owns a specimen" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "hospital owns a laboratory facility" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1834-3856" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-03-29T16:57:03Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017009", + "lbl" : "is owned by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of the owns relation." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "freezer is owned by a biobank organization" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1834-3856" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1909-9269" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-03-29T17:06:06Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -12879,6 +13011,40 @@ "val" : "2024-02-01T10:09:59Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -14988,6 +15154,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0001-8314-2140", + "lbl" : "Raymund Stefancsik", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0001-8910-9851", "lbl" : "Lynn Schriml", @@ -14998,6 +15174,16 @@ "val" : "researcher, metadata, diseases, University of Maryland" } ] } + }, { + "id" : "https://orcid.org/0000-0001-9625-1899", + "lbl" : "William D Duncan", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-2908-3327", "lbl" : "Anne Thessen", @@ -15088,6 +15274,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-8844-9165", + "lbl" : "Damion M Dooley", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-8844-9165)" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1617-8244", "lbl" : "Lindsay G Cowell", @@ -15108,6 +15304,16 @@ "val" : "Canadian biocurator" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1834-3856", + "lbl" : "Mathias Brochhausen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1909-9269", "lbl" : "S. Clint Dowland", @@ -15128,6 +15334,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-2620-0345", + "lbl" : "Asiyah Yu Lin", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-2620-0345" + } ] + } }, { "id" : "https://orcid.org/0000-0003-3138-4118", "lbl" : "Jorrit Poelen", @@ -16404,7 +16620,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -16448,15 +16664,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002472", "pred" : "subPropertyOf", @@ -17625,6 +17841,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -18353,6 +18577,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008507", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008508" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0009006", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0009007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0010001", "pred" : "inverseOf", @@ -18377,6 +18605,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0015001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0015002" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0017008", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0017009" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0018002", "pred" : "inverseOf", diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index dd45dd89..06a83569 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -18,7 +18,7 @@ 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 "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-24" xsd:string [Typedef] id: BFO:0000050 @@ -1929,6 +1929,7 @@ is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002444 name: parasite_of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] synonym: "direct parasite of" EXACT [] is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002454 ! has host @@ -1937,6 +1938,7 @@ inverse_of: RO:0002445 ! parasitized by [Typedef] id: RO:0002445 name: parasitized_by +def: "Inverse of parasite of" [] synonym: "directly parasitized by" EXACT [] is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002453 ! host of @@ -2012,7 +2014,8 @@ is_a: RO:0002442 ! mutualistically interacts with [Typedef] id: RO:0002457 name: acquires_nutrients_from -is_a: RO:0002438 ! trophically interacts with +def: "Inverse of provides nutrients for" [] +is_a: RO:0002437 ! biotically interacts with inverse_of: RO:0002469 ! provides nutrients for [Typedef] @@ -2074,17 +2077,20 @@ is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002469 name: provides_nutrients_for -is_a: RO:0002438 ! trophically interacts with +def: "A biotic interaction where a material entity provides nutrition for an organism." [] +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002470 name: eats -is_a: RO:0002438 ! trophically interacts with +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002471 name: is_eaten_by -is_a: RO:0002438 ! trophically interacts with +def: "Inverse of eats" [] +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002472 @@ -2493,12 +2499,14 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002556 name: pathogen_of +def: "Inverse of has pathogen" [] is_a: RO:0002454 ! has host inverse_of: RO:0002557 ! has pathogen [Typedef] id: RO:0002557 name: has_pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] is_a: RO:0002453 ! host of [Typedef] @@ -3323,6 +3331,17 @@ name: has_primary_substance_added def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] is_a: RO:0009001 ! has substance added +[Typedef] +id: RO:0009006 +name: assay_measures_characteristic +def: "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." [] +inverse_of: RO:0009007 ! characteristic measured by assay + +[Typedef] +id: RO:0009007 +name: characteristic_measured_by_assay +def: "Inverse of 'assay measures characteristic'" [] + [Typedef] id: RO:0009501 name: realized_in_response_to @@ -3720,6 +3739,22 @@ 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:0017006 +name: has_maximum_capacity +def: "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." [] + +[Typedef] +id: RO:0017008 +name: owns +def: "A primitive relation that holds between entities x and y in which y is at x's full disposal." [] +inverse_of: RO:0017009 ! is owned by + +[Typedef] +id: RO:0017009 +name: is_owned_by +def: "Inverse of the owns relation." [] + [Typedef] id: RO:0018001 name: is_myristoyltransferase_activity @@ -3878,6 +3913,20 @@ def: "x directly supplies and drains y if and only if x is a capillary, y is an is_a: RO:0002178 ! supplies is_a: RO:0002179 ! drains +[Typedef] +id: RO:0020202 +name: has_numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0020203 +name: has_denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +is_a: BFO:0000051 ! has part + [Typedef] id: RO:0040035 name: disease_relationship diff --git a/subsets/ro-chado.owl b/subsets/ro-chado.owl index 76b4fd58..48dcd16e 100644 --- a/subsets/ro-chado.owl +++ b/subsets/ro-chado.owl @@ -20,8 +20,8 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2024-02-13 + + 2024-04-24 @@ -1527,7 +1527,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - part of part of @@ -1557,7 +1556,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has part has part @@ -1681,7 +1679,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -1739,9 +1736,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - has characteristic has characteristic - https://github.com/oborel/obo-relations/pull/284 @@ -1781,7 +1776,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant has participant @@ -4132,10 +4126,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + has component participant @@ -4992,7 +4986,6 @@ 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 @@ -6229,6 +6222,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes direct parasite of @@ -6244,6 +6238,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -6430,8 +6425,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. @@ -6568,7 +6564,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. provides nutrients for @@ -6579,7 +6576,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with @@ -6591,7 +6589,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -7505,6 +7504,7 @@ the a supports either the existence of b, or the truth value of b. + Inverse of has pathogen pathogen of @@ -7516,6 +7516,7 @@ the a supports either the existence of b, or the truth value of b. + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member has pathogen @@ -9257,6 +9258,30 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material. + A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic. + + 2023-05-23T15:24:15Z + assay measures characteristic + + + + + + + + Inverse of 'assay measures characteristic' + + 2023-05-23T15:29:50Z + characteristic measured by assay + + + + @@ -10093,10 +10118,10 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 + + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -10143,6 +10168,50 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + anticoagulant-containing test tube has maximum capacity 10 ml. + A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume. + + + has maximum capacity + + + + + + + + + biobank organization owns a specimen + hospital owns a laboratory facility + A primitive relation that holds between entities x and y in which y is at x's full disposal. + + + + This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal. + 2023-03-29T16:57:03Z + owns + + + + + + + + freezer is owned by a biobank organization + Inverse of the owns relation. + + + + 2023-03-29T17:06:06Z + + is owned by + + + + @@ -10551,6 +10620,30 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + A relationship between a ratio or proportion and its dividend. + + has dividend + has numerator + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + has divisor + has denominator + + + + @@ -12457,6 +12550,27 @@ binary, and takes no temporal argument. + + + + researcher + Raymund Stefancsik + + + + + researcher + + + + + + Raymund Stefancsik + + + + + @@ -12478,6 +12592,27 @@ binary, and takes no temporal argument. + + + + researcher + William D Duncan + + + + + researcher + + + + + + William D Duncan + + + + + @@ -12667,6 +12802,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-8844-9165) + Damion M Dooley + + + + + researcher (ORCID 0000-0002-8844-9165) + + + + + + Damion M Dooley + + + + + @@ -12709,6 +12865,27 @@ binary, and takes no temporal argument. + + + + researcher + Mathias Brochhausen + + + + + researcher + + + + + + Mathias Brochhausen + + + + + @@ -12751,6 +12928,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0003-2620-0345 + Asiyah Yu Lin + + + + + Researcher ORCID=0000-0003-2620-0345 + + + + + + Asiyah Yu Lin + + + + + @@ -13259,15 +13457,15 @@ No imports - - - + + + @@ -13277,15 +13475,15 @@ No imports - - - + + + @@ -13473,9 +13671,9 @@ No imports - - - + + + @@ -13484,9 +13682,9 @@ No imports - - - + + + @@ -13518,9 +13716,9 @@ No imports - + - + @@ -13529,9 +13727,9 @@ No imports - + - + @@ -13563,9 +13761,9 @@ No imports - + - + @@ -13574,9 +13772,9 @@ No imports - + - + @@ -13608,9 +13806,9 @@ No imports - + - + @@ -13619,9 +13817,9 @@ No imports - + - + @@ -13653,9 +13851,9 @@ No imports - + - + @@ -13664,9 +13862,9 @@ No imports - + - + @@ -13697,7 +13895,7 @@ No imports - + @@ -13708,7 +13906,7 @@ No imports - + @@ -13741,9 +13939,9 @@ No imports - - - + + + @@ -13752,9 +13950,9 @@ No imports - - - + + + @@ -13785,9 +13983,9 @@ No imports - - - + + + @@ -13796,9 +13994,9 @@ No imports - - - + + + @@ -13829,9 +14027,9 @@ No imports - - - + + + @@ -13840,9 +14038,9 @@ No imports - - - + + + @@ -13873,9 +14071,9 @@ No imports - - - + + + @@ -13884,9 +14082,9 @@ No imports - - - + + + @@ -13918,8 +14116,8 @@ No imports - - + + @@ -13929,8 +14127,8 @@ No imports - - + + diff --git a/subsets/ro-developmental.json b/subsets/ro-developmental.json index d6d32493..006ef119 100644 --- a/subsets/ro-developmental.json +++ b/subsets/ro-developmental.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 6518ba78..d6bae920 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index 5f2ee16a..0fd9be78 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + diff --git a/subsets/ro-developmental.tsv b/subsets/ro-developmental.tsv index 3095b994..de55b64b 100644 --- a/subsets/ro-developmental.tsv +++ b/subsets/ro-developmental.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid1 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid18 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid22 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid26 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid33 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid37 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid40 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid5 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid52 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid58 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid61 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid64 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid67 -_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid9 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid1 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid18 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid22 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid26 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid33 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid37 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid40 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid5 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid52 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid58 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid61 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid64 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid67 +_:B3d8b6862X2D8849X2D4c84X2Dbf8dX2D4680b61a54e1genid9 @@ -39,6 +39,7 @@ _:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid9 + diff --git a/subsets/ro-interaction.json b/subsets/ro-interaction.json index 63fc49ba..35526c31 100644 --- a/subsets/ro-interaction.json +++ b/subsets/ro-interaction.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 122c9d98..43c72c85 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index 6c96e01f..bb09791e 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + diff --git a/subsets/ro-interaction.tsv b/subsets/ro-interaction.tsv index 8318d6a8..0d17032c 100644 --- a/subsets/ro-interaction.tsv +++ b/subsets/ro-interaction.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid1 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid18 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid22 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid26 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid33 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid37 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid40 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid5 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid52 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid58 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid61 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid64 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid67 -_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid9 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid1 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid18 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid22 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid26 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid33 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid37 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid40 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid5 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid52 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid58 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid61 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid64 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid67 +_:B24b64a74X2D2229X2D4fa8X2Dad19X2D7e1c2a09388agenid9 @@ -39,6 +39,7 @@ _:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid9 + diff --git a/subsets/ro-mereotopology.json b/subsets/ro-mereotopology.json index d0fdda09..6ed77fde 100644 --- a/subsets/ro-mereotopology.json +++ b/subsets/ro-mereotopology.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 31d0bd7e..41ec74b6 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index b0654e52..9938010f 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + diff --git a/subsets/ro-mereotopology.tsv b/subsets/ro-mereotopology.tsv index 87955ff5..082be7e9 100644 --- a/subsets/ro-mereotopology.tsv +++ b/subsets/ro-mereotopology.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid1 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid18 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid22 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid26 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid33 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid37 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid40 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid5 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid52 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid58 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid61 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid64 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid67 -_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid9 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid1 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid18 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid22 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid26 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid33 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid37 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid40 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid5 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid52 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid58 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid61 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid64 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid67 +_:Bd6eb0496X2D5952X2D4af9X2Db98bX2Dd452cbfde917genid9 @@ -39,6 +39,7 @@ _:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid9 + diff --git a/subsets/ro-sequence.json b/subsets/ro-sequence.json index 2cfc531b..dc34328e 100644 --- a/subsets/ro-sequence.json +++ b/subsets/ro-sequence.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 bbbc3979..542548c2 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index 359bce8a..8355f3bf 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + diff --git a/subsets/ro-sequence.tsv b/subsets/ro-sequence.tsv index aabcd030..41d67ec5 100644 --- a/subsets/ro-sequence.tsv +++ b/subsets/ro-sequence.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid1 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid18 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid22 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid26 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid33 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid37 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid40 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid5 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid52 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid58 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid61 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid64 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid67 -_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid9 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid1 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid18 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid22 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid26 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid33 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid37 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid40 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid5 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid52 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid58 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid61 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid64 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid67 +_:B57fe547aX2D86b1X2D4374X2D8797X2Dcc72b24603edgenid9 @@ -39,6 +39,7 @@ _:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid9 + diff --git a/subsets/ro-time-interval.json b/subsets/ro-time-interval.json index 4acf12c3..7c5d6f3f 100644 --- a/subsets/ro-time-interval.json +++ b/subsets/ro-time-interval.json @@ -241,9 +241,6 @@ }, { "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" } ] } }, { @@ -3143,11 +3140,11 @@ "val" : "RO:0002238" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component_participant" @@ -6066,6 +6063,9 @@ "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A parasite-host relationship where an organism benefits at the expense of another." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6096,6 +6096,9 @@ "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of parasite of" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6404,6 +6407,9 @@ "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of provides nutrients for" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002457" @@ -6553,6 +6559,9 @@ "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where a material entity provides nutrition for an organism." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002469" @@ -6570,6 +6579,9 @@ "lbl" : "eats", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002470" @@ -6590,6 +6602,9 @@ "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of eats" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002471" @@ -7669,6 +7684,9 @@ "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Inverse of has pathogen" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002556" @@ -7686,6 +7704,9 @@ "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "RO:0002557" @@ -11310,6 +11331,52 @@ "val" : "directly_supplies_and_drains" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020202", + "lbl" : "has numerator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its dividend." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has dividend" + } ], + "xrefs" : [ { + "val" : "RO:0020202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_numerator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020203", + "lbl" : "has denominator", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a ratio or proportion and its divisor." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has divisor" + } ], + "xrefs" : [ { + "val" : "RO:0020203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8314-2140" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_denominator" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -12533,7 +12600,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002457", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", @@ -12561,15 +12628,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002470", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002471", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002473", "pred" : "subPropertyOf", @@ -13566,6 +13633,14 @@ "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_0020202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020203", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13961,7 +14036,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -14354,6 +14429,14 @@ "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_0020202", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020203", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0001470" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] }, { "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 54ead77f..365558a6 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -21,11 +21,12 @@ inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco xref: RO:0002457 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with inverse_of: provides_nutrients_for ! provides nutrients for [Typedef] @@ -1451,11 +1452,12 @@ inverse_of: starts_during ! starts during [Typedef] id: eats name: eats +def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." [] subset: ro-eco xref: RO:0002470 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: ecologically_co-occurs_with @@ -1791,7 +1793,6 @@ 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 @@ -1829,7 +1830,7 @@ id: has_component_participant name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] xref: RO:0002238 -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: has_participant ! has participant @@ -1861,6 +1862,17 @@ property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Proper property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: has_denominator +name: has denominator +def: "A relationship between a ratio or proportion and its divisor." [] +synonym: "has divisor" EXACT [] +xref: RO:0020203 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_developmental_contribution_from name: has developmental contribution from @@ -2297,6 +2309,17 @@ is_a: negatively_regulated_by ! negatively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z +[Typedef] +id: has_numerator +name: has numerator +def: "A relationship between a ratio or proportion and its dividend." [] +synonym: "has dividend" EXACT [] +xref: RO:0020202 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +domain: PATO:0001470 +range: PATO:0000001 +is_a: has_part ! has part + [Typedef] id: has_output name: has output @@ -2383,12 +2406,12 @@ 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] id: has_pathogen name: has pathogen +def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" [] subset: ro-eco xref: RO:0002557 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -3309,12 +3332,13 @@ inverse_of: is_downstream_of_sequence_of ! is downstream of sequence of [Typedef] id: is_eaten_by name: is eaten by +def: "Inverse of eats" [] subset: ro-eco xref: RO:0002471 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: is_end_sequence_of @@ -3743,6 +3767,7 @@ is_a: sequentially_related_to ! sequentially related to [Typedef] id: parasite_of name: parasite of +def: "A parasite-host relationship where an organism benefits at the expense of another." [] subset: ro-eco synonym: "direct parasite of" EXACT [] xref: RO:0002444 @@ -3757,6 +3782,7 @@ inverse_of: parasitized_by ! parasitized by [Typedef] id: parasitized_by name: parasitized by +def: "Inverse of parasite of" [] subset: ro-eco synonym: "directly parasitized by" EXACT [] xref: RO:0002445 @@ -3887,6 +3913,7 @@ is_a: participates_in ! participates in [Typedef] id: pathogen_of name: pathogen of +def: "Inverse of has pathogen" [] subset: ro-eco xref: RO:0002556 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -4088,10 +4115,11 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: provides_nutrients_for name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: trophically_interacts_with ! trophically interacts with +is_a: biotically_interacts_with ! biotically interacts with [Typedef] id: quality_of diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index a8cde506..7efe6116 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -278,7 +278,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of - part of part of @@ -310,7 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part - has part has part @@ -390,9 +388,7 @@ 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 @@ -420,7 +416,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant this blood coagulation has participant this blood clot @@ -432,7 +427,6 @@ 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 @@ -2530,10 +2524,10 @@ N1 SubclassOf ( X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + RO:0002238 has_component_participant has component participant @@ -3352,7 +3346,6 @@ 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 @@ -4522,6 +4515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Pediculus humanus capitis parasite of human + A parasite-host relationship where an organism benefits at the expense of another. parasitizes RO:0002444 @@ -4539,6 +4533,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + Inverse of parasite of has parasite parasitised by @@ -4736,8 +4731,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of provides nutrients for Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 @@ -4838,7 +4834,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where a material entity provides nutrition for an organism. RO:0002469 @@ -4851,7 +4848,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with RO:0002470 @@ -4865,7 +4863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + + Inverse of eats eaten by is target of eating interaction with @@ -5583,6 +5582,7 @@ For example, A and B may be gene products and binding of B by A positively regul + Inverse of has pathogen RO:0002556 @@ -5596,6 +5596,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member RO:0002557 @@ -8203,6 +8204,38 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + A relationship between a ratio or proportion and its dividend. + + RO:0020202 + has dividend + has_numerator + has numerator + + + + + + + + + + + A relationship between a ratio or proportion and its divisor. + + RO:0020203 + has divisor + has_denominator + has denominator + + + + @@ -8398,6 +8431,12 @@ 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 dadfed7a..a51e190e 100644 --- a/subsets/ro-time-interval.tsv +++ b/subsets/ro-time-interval.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid1 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid18 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid22 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid26 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid33 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid37 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid40 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid5 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid52 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid58 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid61 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid64 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid67 -_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid9 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid1 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid18 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid22 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid26 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid33 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid37 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid40 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid5 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid52 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid58 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid61 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid64 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid67 +_:Bdefaa258X2D550cX2D475bX2Da0caX2Ddb19e71e6cb8genid9 @@ -39,6 +39,7 @@ _:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid9 +