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ro-base.json
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ro-base.json
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{
"graphs" : [ {
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/RO_0002170",
"meta" : {
"definition" : {
"val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552"
}, {
"pred" : "http://xmlns.com/foaf/0.1/page",
"val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"
}, {
"pred" : "http://xmlns.com/foaf/0.1/page",
"val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)."
} ]
},
"type" : "PROPERTY",
"lbl" : "connected to"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002291",
"meta" : {
"definition" : {
"val" : "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"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" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part."
} ]
},
"type" : "PROPERTY",
"lbl" : "ubiquitously expressed in"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002292",
"meta" : {
"definition" : {
"val" : "Inverse of 'expressed in'",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
} ]
},
"type" : "PROPERTY",
"lbl" : "expresses"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002171",
"meta" : {
"definition" : {
"val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "non-overlapping with"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000425",
"val" : "Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)"
}, {
"pred" : "http://xmlns.com/foaf/0.1/page",
"val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "shares no parts with"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "http://purl.obolibrary.org/obo/RO_0002163"
} ]
},
"type" : "PROPERTY",
"lbl" : "mutually spatially disjoint with"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002176",
"meta" : {
"definition" : {
"val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "The M8 connects Glasgow and Edinburgh"
}, {
"pred" : "http://xmlns.com/foaf/0.1/page",
"val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552"
}, {
"pred" : "http://xmlns.com/foaf/0.1/page",
"val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)."
} ]
},
"type" : "PROPERTY",
"lbl" : "connects"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002297",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "GOC:mtg_berkeley_2013"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists."
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
"val" : "results_in_formation_of"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"
} ]
},
"type" : "PROPERTY",
"lbl" : "results in formation of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002298",
"meta" : {
"definition" : {
"val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
"val" : "results_in_morphogenesis_of"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "GOC:mtg_berkeley_2013"
} ]
},
"type" : "PROPERTY",
"lbl" : "results in morphogenesis of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002177",
"meta" : {
"definition" : {
"val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.",
"xrefs" : [ ]
}
},
"type" : "PROPERTY",
"lbl" : "attached to part of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002178",
"meta" : {
"definition" : {
"val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205"
} ]
},
"type" : "PROPERTY",
"lbl" : "supplies"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002299",
"meta" : {
"definition" : {
"val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "GOC:mtg_berkeley_2013"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
"val" : "results_in_maturation_of"
} ]
},
"type" : "PROPERTY",
"lbl" : "results in maturation of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002179",
"meta" : {
"definition" : {
"val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205"
} ]
},
"type" : "PROPERTY",
"lbl" : "drains"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002172",
"meta" : {
"definition" : {
"val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints"
} ]
},
"type" : "PROPERTY",
"lbl" : "taxonomic class assertion"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002293",
"meta" : {
"definition" : {
"val" : "inverse of ubiquiotously expressed in",
"xrefs" : [ ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
} ]
},
"type" : "PROPERTY",
"lbl" : "ubiquitously expresses"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002173",
"meta" : {
"definition" : {
"val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints"
} ]
},
"type" : "PROPERTY",
"lbl" : "ambiguous for taxon"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002295",
"meta" : {
"definition" : {
"val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
"val" : "results_in_developmental_progression_of"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "http://wiki.geneontology.org/index.php/Ontology_extensions"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
} ]
},
"type" : "PROPERTY",
"lbl" : "results in developmental progression of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002174",
"meta" : {
"definition" : {
"val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.",
"xrefs" : [ ]
},
"comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "https://orcid.org/0000-0002-6601-2165"
} ]
},
"type" : "PROPERTY",
"lbl" : "dubious for taxon"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002175",
"meta" : {
"definition" : {
"val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "https://orcid.org/0000-0002-6601-2165"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552"
} ]
},
"type" : "PROPERTY",
"lbl" : "present in taxon"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002296",
"meta" : {
"definition" : {
"val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
"val" : "results_in_development_of"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.geneontology.org/GO.doc.development.shtml"
} ]
},
"type" : "PROPERTY",
"lbl" : "results in development of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002160",
"meta" : {
"definition" : {
"val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947"
}, {
"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" : "Chris Mungall"
} ]
},
"type" : "PROPERTY",
"lbl" : "only in taxon"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002286",
"meta" : {
"definition" : {
"val" : "Inverse of developmentally preceded by",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
} ]
},
"type" : "PROPERTY",
"lbl" : "developmentally succeeded by"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002287",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue"
} ]
},
"type" : "PROPERTY",
"lbl" : "part of developmental precursor of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002161",
"meta" : {
"definition" : {
"val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000425",
"val" : "?X DisjointWith RO_0002162 some ?Y "
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "tooth SubClassOf 'never in taxon' value 'Aves'"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
} ]
},
"type" : "PROPERTY",
"lbl" : "never in taxon"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002162",
"meta" : {
"definition" : {
"val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.",
"xrefs" : [ ]
},
"comments" : [ "Connects a biological entity to its taxon of origin." ],
"subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
"basicPropertyValues" : [ {
"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" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Jennifer Deegan"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints"
} ]
},
"type" : "PROPERTY",
"lbl" : "in taxon"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002163",
"meta" : {
"definition" : {
"val" : "A is spatially_disjoint_from B if and only if they have no parts in common",
"xrefs" : [ ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000424",
"val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0001900",
"val" : "http://purl.obolibrary.org/obo/RO_0001901"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
"val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. "
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://xmlns.com/foaf/0.1/page",
"val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
} ]
},
"type" : "PROPERTY",
"lbl" : "spatially disjoint from"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002285",
"meta" : {
"definition" : {
"val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "replaces"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"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" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage"
} ]
},
"type" : "PROPERTY",
"lbl" : "developmentally replaces"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002158",
"meta" : {
"definition" : {
"val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.",
"xrefs" : [ ]
},
"comments" : [ "VBO calls this homologous_to" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
"val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
} ]
},
"type" : "PROPERTY",
"lbl" : "shares ancestor with"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002159",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
} ]
},
"type" : "PROPERTY",
"lbl" : "serially homologous to"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0000092",
"meta" : {
"definition" : {
"val" : "inverse of has disposition",
"xrefs" : [ ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ]
},
"type" : "PROPERTY",
"lbl" : "disposition of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0000091",
"meta" : {
"definition" : {
"val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence",
"xrefs" : [ ]
}
},
"type" : "PROPERTY",
"lbl" : "has disposition"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0003002",
"meta" : {
"definition" : {
"val" : "Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Logical axioms to be added after the relevant branch of GO is MIREOTed in"
} ]
},
"type" : "PROPERTY",
"lbl" : "represses expression of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0003001",
"meta" : {
"definition" : {
"val" : "a produced_by b iff some process that occurs_in b has_output a.",
"xrefs" : [ ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
"basicPropertyValues" : [ {
"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" : "Melissa Haendel"
} ]
},
"type" : "PROPERTY",
"lbl" : "produced by"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002156",
"meta" : {
"definition" : {
"val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "ancestral_stucture_of"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "evolutionarily_descended_from"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
} ]
},
"type" : "PROPERTY",
"lbl" : "derived by descent from"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002157",
"meta" : {
"definition" : {
"val" : "inverse of derived by descent from",
"xrefs" : [ ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
} ]
},
"type" : "PROPERTY",
"lbl" : "has derived by descendant"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0003003",
"meta" : {
"definition" : {
"val" : "Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Logical axioms to be added after the relevant branch of GO is MIREOTed in"
} ]
},
"type" : "PROPERTY",
"lbl" : "increases expression of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002150",
"meta" : {
"definition" : {
"val" : "X continuous_with Y if and only if X and Y share a fiat boundary.",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
"val" : "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)"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0001900",
"val" : "http://purl.obolibrary.org/obo/RO_0001901"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "David Osumi-Sutherland"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "connected to"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "FMA:85972"
} ]
},
"type" : "PROPERTY",
"lbl" : "continuous with"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002151",
"meta" : {
"definition" : {
"val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x",
"xrefs" : [ ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000426",
"val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "proper overlaps"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0001900",
"val" : "http://purl.obolibrary.org/obo/RO_0001901"
} ]
},
"type" : "PROPERTY",
"lbl" : "partially overlaps"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0003000",
"meta" : {
"definition" : {
"val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.",
"xrefs" : [ ]
},
"comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ],
"subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Melissa Haendel"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000125"
} ]
},
"type" : "PROPERTY",
"lbl" : "produces"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002026",
"meta" : {
"definition" : {
"val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.",
"xrefs" : [ "GOC:dos" ]
},
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
"val" : "2017-12-07T12:58:06Z"
}, {
"pred" : "ttp://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "dos"
} ]
},
"type" : "PROPERTY",
"lbl" : "in register with"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002380",
"meta" : {
"definition" : {
"val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y",
"xrefs" : [ ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ],
"basicPropertyValues" : [ {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "FMA:85994"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000428"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
} ]
},
"type" : "PROPERTY",
"lbl" : "branching part of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0000081",
"meta" : {
"definition" : {
"val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this investigator role is a role of this person"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "is role of"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "role_of"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."
} ]
},
"type" : "PROPERTY",
"lbl" : "role of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0000080",
"meta" : {
"definition" : {
"val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "quality_of"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "A quality inheres in its bearer at all times for which the quality exists."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "is quality of"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this red color is a quality of this apple"
} ]
},
"type" : "PROPERTY",
"lbl" : "quality of"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0000085",
"meta" : {
"definition" : {
"val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "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."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "has_function"
} ]
},
"type" : "PROPERTY",
"lbl" : "has function"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002264",
"meta" : {
"definition" : {
"val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.",
"xrefs" : [ ]
},
"synonyms" : [ {
"pred" : "hasRelatedSynonym",
"val" : "affects",
"xrefs" : [ ]
} ],
"basicPropertyValues" : [ {
"pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
"val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway."
} ]
},
"type" : "PROPERTY",
"lbl" : "acts upstream of or within"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002385",
"meta" : {
"definition" : {
"val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000428"
} ]
},
"type" : "PROPERTY",
"lbl" : "has potential to developmentally contribute to"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002022",
"meta" : {
"comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
"val" : "2017-09-17T13:52:24Z"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "dos"
} ]
},
"type" : "PROPERTY",
"lbl" : "directly regulated by"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002023",
"meta" : {
"definition" : {
"val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.",
"xrefs" : [ "GOC:dos" ]
},
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "dos"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
"val" : "2017-09-17T13:52:38Z"
} ]
},
"type" : "PROPERTY",
"lbl" : "directly negatively regulated by"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002386",
"meta" : {
"definition" : {
"val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000428"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
} ]
},
"type" : "PROPERTY",
"lbl" : "has potential to developmentally induce"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002024",
"meta" : {
"definition" : {
"val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.",
"xrefs" : [ "GOC:dos" ]
},
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
"val" : "2017-09-17T13:52:47Z"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
"val" : "dos"
} ]
},
"type" : "PROPERTY",
"lbl" : "directly positively regulated by"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002387",
"meta" : {
"definition" : {
"val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y",
"xrefs" : [ ]
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/IAO_0000428"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Chris Mungall"
} ]
},
"type" : "PROPERTY",
"lbl" : "has potential to develop into"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002388",
"meta" : {