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ro-full.json
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{
"graphs" : [ {
"id" : "http://purl.obolibrary.org/obo/ro/ro-full.json",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.org/dc/terms/description",
"val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies."
}, {
"pred" : "http://purl.org/dc/terms/license",
"val" : "https://creativecommons.org/publicdomain/zero/1.0/"
}, {
"pred" : "http://purl.org/dc/terms/title",
"val" : "OBO Relations Ontology"
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2023-08-18"
}, {
"pred" : "http://xmlns.com/foaf/0.1/homepage",
"val" : " https://github.com/oborel/obo-relations/"
} ],
"version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro-full.json"
},
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/IAO_0000125",
"lbl" : "pending final vetting",
"type" : "INDIVIDUAL",
"meta" : {
"definition" : {
"val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "pending final vetting"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/IAO_0000078",
"lbl" : "curation status specification",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "curation status specification"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "PERSON:Bill Bug"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "OBI_0000266"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/IAO_0000428",
"lbl" : "requires discussion",
"type" : "INDIVIDUAL",
"meta" : {
"definition" : {
"val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "requires discussion"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Alan Ruttenberg"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "group:OBI"
} ]
}
}, {
"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",
"meta" : {
"definition" : {
"val" : "a core relation that holds between a part and its whole"
},
"subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "is part of"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "my brain is part of my body (continuant parthood, two material entities)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this day is part of this year (occurrent parthood)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "part_of"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0001900",
"val" : "http://purl.obolibrary.org/obo/RO_0001901"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0040042",
"val" : "http://purl.obolibrary.org/obo/BFO_0000002"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0040042",
"val" : "http://purl.obolibrary.org/obo/BFO_0000003"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0040042",
"val" : "http://purl.obolibrary.org/obo/BFO_0000004"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0040042",
"val" : "http://purl.obolibrary.org/obo/BFO_0000017"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0040042",
"val" : "http://purl.obolibrary.org/obo/BFO_0000019"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0040042",
"val" : "http://purl.obolibrary.org/obo/BFO_0000020"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0040042",
"val" : "http://purl.obolibrary.org/obo/BFO_0000031"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "https://wiki.geneontology.org/Part_of"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000051",
"lbl" : "has part",
"type" : "PROPERTY",
"meta" : {
"definition" : {
"val" : "a core relation that holds between a whole and its part"
},
"subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "has part"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "my body has part my brain (continuant parthood, two material entities)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this year has part this day (occurrent parthood)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "has_part"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0001900",
"val" : "http://purl.obolibrary.org/obo/RO_0001901"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000054",
"lbl" : "realized in",
"type" : "PROPERTY",
"meta" : {
"comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "realized in"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this disease is realized in this disease course"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this fragility is realized in this shattering"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this investigator role is realized in this investigation"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "is realized by"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "realized_in"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "[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])"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000055",
"lbl" : "realizes",
"type" : "PROPERTY",
"meta" : {
"comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "realizes"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this disease course realizes this disease"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this investigation realizes this investigator role"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this shattering realizes this fragility"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "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])"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/iao.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000060",
"lbl" : "obsolete preceded by",
"type" : "PROPERTY",
"meta" : {
"comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ],
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000062",
"lbl" : "preceded by",
"type" : "PROPERTY",
"meta" : {
"definition" : {
"val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), 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."
},
"subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "preceded by"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "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."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "is preceded by"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "preceded_by"
}, {
"pred" : "http://purl.org/dc/terms/source",
"val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000063",
"lbl" : "precedes",
"type" : "PROPERTY",
"meta" : {
"definition" : {
"val" : "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."
},
"subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "precedes"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000066",
"lbl" : "occurs in",
"type" : "PROPERTY",
"meta" : {
"definition" : {
"val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"
},
"comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ],
"subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "occurs in"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "occurs_in"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "unfolds in"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "unfolds_in"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "https://wiki.geneontology.org/Occurs_in"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000067",
"lbl" : "contains process",
"type" : "PROPERTY",
"meta" : {
"definition" : {
"val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"
},
"comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
"val" : "site of"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"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/CL_0000000",
"lbl" : "cell",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.",
"xrefs" : [ "CARO:mah" ]
},
"comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ],
"xrefs" : [ {
"val" : "CALOHA:TS-2035"
}, {
"val" : "FBbt:00007002"
}, {
"val" : "FMA:68646"
}, {
"val" : "GO:0005623"
}, {
"val" : "KUPO:0000002"
}, {
"val" : "MESH:D002477"
}, {
"val" : "VHOG:0001533"
}, {
"val" : "WBbt:0004017"
}, {
"val" : "XAO:0003012"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/CL_0000101",
"lbl" : "sensory neuron",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "Any neuron having a sensory function; an afferent neuron conveying sensory impulses.",
"xrefs" : [ "ISBN:0721662544" ]
},
"xrefs" : [ {
"val" : "BTO:0001037"
}, {
"val" : "FBbt:00005124"
}, {
"val" : "FMA:84649"
}, {
"val" : "MESH:D011984"
}, {
"val" : "WBbt:0005759"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/CL_0000540",
"lbl" : "neuron",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.",
"xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ]
},
"comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "nerve cell"
} ],
"xrefs" : [ {
"val" : "BTO:0000938"
}, {
"val" : "CALOHA:TS-0683"
}, {
"val" : "FBbt:00005106"
}, {
"val" : "FMA:54527"
}, {
"val" : "VHOG:0001483"
}, {
"val" : "WBbt:0003679"
} ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/RO_0002175",
"val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/ENVO_01000254",
"lbl" : "environmental system",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A system which has the disposition to environ one or more material entities.",
"xrefs" : [ "DOI:10.1186/2041-1480-4-43" ]
},
"comments" : [ "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised." ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "environment"
} ],
"xrefs" : [ {
"val" : "EcoLexicon:environment"
} ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
"val" : "2013-09-23T16:04:08Z"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/ENVO_01000739",
"lbl" : "habitat",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An environmental system which can sustain and allow the growth of an ecological population.",
"xrefs" : [ "EnvO:EnvO" ]
},
"comments" : [ "A habitat's specificity to an ecological population differentiates it from other environment classes." ],
"xrefs" : [ {
"val" : "EcoLexicon:habitat"
}, {
"val" : "LTER:238"
}, {
"val" : "SWEETRealm:Habitat"
}, {
"val" : "https://en.wikipedia.org/wiki/Habitat"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/ENVO_01003004",
"lbl" : "derives from part of",
"type" : "PROPERTY",
"meta" : {
"definition" : {
"val" : "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity."
}
}
}, {
"id" : "http://purl.obolibrary.org/obo/GO_0003674",
"lbl" : "molecular_function",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.",
"xrefs" : [ "GOC:pdt" ]
},
"comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "molecular function"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GO_0004842",
"lbl" : "ubiquitin-protein transferase activity",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.",
"xrefs" : [ "GOC:BioGRID", "GOC:jh2", "PMID:9635407" ]
},
"synonyms" : [ {
"pred" : "hasBroadSynonym",
"val" : "E2"
}, {
"pred" : "hasBroadSynonym",
"val" : "E3"
}, {
"pred" : "hasNarrowSynonym",
"val" : "ubiquitin conjugating enzyme activity"
}, {
"pred" : "hasNarrowSynonym",
"val" : "ubiquitin ligase activity"
}, {
"pred" : "hasNarrowSynonym",
"val" : "ubiquitin protein ligase activity"
}, {
"pred" : "hasNarrowSynonym",
"val" : "ubiquitin protein-ligase activity"
}, {
"pred" : "hasNarrowSynonym",
"val" : "ubiquitin-conjugating enzyme activity"
} ],
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}
}, {
"id" : "http://purl.obolibrary.org/obo/GO_0005634",
"lbl" : "nucleus",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.",
"xrefs" : [ "GOC:go_curators" ]
},
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "cell nucleus"
}, {
"pred" : "hasNarrowSynonym",
"val" : "horsetail nucleus",
"xrefs" : [ "GOC:al", "GOC:mah", "GOC:vw", "PMID:15030757" ]
} ],
"xrefs" : [ {
"val" : "NIF_Subcellular:sao1702920020"
}, {
"val" : "Wikipedia:Cell_nucleus"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GO_0008150",
"lbl" : "biological_process",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.",
"xrefs" : [ "GOC:pdt" ]
},
"comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "biological process"
}, {
"pred" : "hasExactSynonym",
"val" : "physiological process"
}, {
"pred" : "hasRelatedSynonym",
"val" : "single organism process"
}, {
"pred" : "hasRelatedSynonym",
"val" : "single-organism process"
} ],
"xrefs" : [ {
"val" : "Wikipedia:Biological_process"
} ],
"basicPropertyValues" : [ {
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"val" : "jl"
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"val" : "2012-09-19T15:05:24Z"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GO_0016301",
"lbl" : "kinase activity",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.",
"xrefs" : [ "ISBN:0198506732" ]
},
"comments" : [ "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term." ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "phosphokinase activity"
} ],
"xrefs" : [ {
"val" : "Reactome:R-HSA-6788855"
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"val" : "Reactome:R-HSA-6788867"
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}
}, {
"id" : "http://purl.obolibrary.org/obo/GO_0019107",
"lbl" : "myristoyltransferase activity",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.",
"xrefs" : [ "GOC:ai" ]
},
"xrefs" : [ {
"val" : "Reactome:R-HSA-141367"
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"val" : "Reactome:R-HSA-162914"
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}
}, {
"id" : "http://purl.obolibrary.org/obo/IAO_0000002",
"lbl" : "example to be eventually removed",
"type" : "INDIVIDUAL",
"meta" : {
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"pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
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}, {