{ "graphs" : [ { "id" : "http://purl.obolibrary.org/obo/ro.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" : "2024-02-13" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro.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:" }, { "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." ], "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/OBOFoundry/COB/issues/65" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", "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 that has a plasma membrane and results from cellular division." }, "comments" : [ "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.", "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).", "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism." ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { "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/COB_0000121", "lbl" : "measurement datum", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/COB_0001000", "lbl" : "exposure of organism", "type" : "CLASS", "meta" : { "definition" : { "val" : "A process during which an organism comes into contact with another entity." } } }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", "lbl" : "environmental system", "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.", "This is the same as GO molecular function" ], "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" } ], "xrefs" : [ { "val" : "KEGG_REACTION:R03876" }, { "val" : "Reactome:R-HSA-1169394" }, { "val" : "Reactome:R-HSA-1169395" }, { "val" : "Reactome:R-HSA-1169397" }, { "val" : "Reactome:R-HSA-1169398" }, { "val" : "Reactome:R-HSA-1169402" }, { "val" : "Reactome:R-HSA-1169405" }, { "val" : "Reactome:R-HSA-1169406" }, { "val" : "Reactome:R-HSA-1234163" }, { "val" : "Reactome:R-HSA-1234172" }, { "val" : "Reactome:R-HSA-1253282" }, { "val" : "Reactome:R-HSA-1358789" }, { "val" : "Reactome:R-HSA-1358790" }, { "val" : "Reactome:R-HSA-1358792" }, { "val" : "Reactome:R-HSA-1363331" }, { "val" : "Reactome:R-HSA-168915" }, { "val" : "Reactome:R-HSA-173542" }, { "val" : "Reactome:R-HSA-173545" }, { "val" : "Reactome:R-HSA-174057" }, { "val" : "Reactome:R-HSA-174104" }, { "val" : "Reactome:R-HSA-174144" }, { "val" : "Reactome:R-HSA-174159" }, { "val" : "Reactome:R-HSA-174195" }, { "val" : "Reactome:R-HSA-174227" }, { 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"Reactome:R-HSA-2179276" }, { "val" : "Reactome:R-HSA-2186747" }, { "val" : "Reactome:R-HSA-2186785" }, { "val" : "Reactome:R-HSA-2187368" }, { "val" : "Reactome:R-HSA-2213017" }, { "val" : "Reactome:R-HSA-264444" }, { "val" : "Reactome:R-HSA-2682349" }, { "val" : "Reactome:R-HSA-2730904" }, { "val" : "Reactome:R-HSA-2737728" }, { "val" : "Reactome:R-HSA-2769007" }, { "val" : "Reactome:R-HSA-2900765" }, { "val" : "Reactome:R-HSA-3000335" }, { "val" : "Reactome:R-HSA-3134804" }, { "val" : "Reactome:R-HSA-3134946" }, { "val" : "Reactome:R-HSA-3249386" }, { "val" : "Reactome:R-HSA-3780995" }, { "val" : "Reactome:R-HSA-3781009" }, { "val" : "Reactome:R-HSA-3788724" }, { "val" : "Reactome:R-HSA-3797226" }, { "val" : "Reactome:R-HSA-400267" }, { "val" : "Reactome:R-HSA-4332236" }, { "val" : "Reactome:R-HSA-446877" }, { "val" : "Reactome:R-HSA-450358" }, { "val" : "Reactome:R-HSA-451418" }, { "val" : "Reactome:R-HSA-5205682" }, { "val" : "Reactome:R-HSA-5357757" }, { "val" : "Reactome:R-HSA-5362412" }, { "val" : "Reactome:R-HSA-5483238" }, { "val" : "Reactome:R-HSA-5607725" }, { "val" : "Reactome:R-HSA-5607728" }, { "val" : "Reactome:R-HSA-5607756" }, { "val" : "Reactome:R-HSA-5607757" }, { "val" : "Reactome:R-HSA-5610742" }, { "val" : "Reactome:R-HSA-5610745" }, { "val" : "Reactome:R-HSA-5610746" }, { "val" : "Reactome:R-HSA-5652009" }, { "val" : "Reactome:R-HSA-5655170" }, { "val" : "Reactome:R-HSA-5660753" }, { "val" : "Reactome:R-HSA-5667107" }, { "val" : "Reactome:R-HSA-5667111" }, { "val" : "Reactome:R-HSA-5668454" }, { "val" : "Reactome:R-HSA-5668534" }, { "val" : "Reactome:R-HSA-5675470" }, { "val" : "Reactome:R-HSA-5684250" }, { "val" : "Reactome:R-HSA-5691108" }, { "val" : "Reactome:R-HSA-5693108" }, { "val" : "Reactome:R-HSA-68712" }, { "val" : "Reactome:R-HSA-69598" }, { "val" : "Reactome:R-HSA-741386" }, { "val" : "Reactome:R-HSA-75824" }, { "val" : "Reactome:R-HSA-870449" }, { "val" : "Reactome:R-HSA-8948709" }, { "val" : "Reactome:R-HSA-8956106" }, { "val" : "Reactome:R-HSA-9013069" }, { "val" : "Reactome:R-HSA-9013974" }, { "val" : "Reactome:R-HSA-9014342" }, { "val" : "Reactome:R-HSA-918224" }, { "val" : "Reactome:R-HSA-936412" }, { "val" : "Reactome:R-HSA-936942" }, { "val" : "Reactome:R-HSA-936986" }, { "val" : "Reactome:R-HSA-9628444" }, { "val" : "Reactome:R-HSA-9645394" }, { "val" : "Reactome:R-HSA-9645414" }, { "val" : "Reactome:R-HSA-9688831" }, { "val" : "Reactome:R-HSA-9701000" }, { "val" : "Reactome:R-HSA-9750946" }, { "val" : "Reactome:R-HSA-975118" }, { "val" : "Reactome:R-HSA-975147" }, { "val" : "Reactome:R-HSA-9758604" }, { "val" : "Reactome:R-HSA-9793444" }, { "val" : "Reactome:R-HSA-9793485" }, { "val" : "Reactome:R-HSA-9793679" }, { "val" : "Reactome:R-HSA-9796346" }, { "val" : "Reactome:R-HSA-9796387" }, { "val" : "Reactome:R-HSA-9796626" }, { "val" : "Reactome:R-HSA-9815507" }, { "val" : "Reactome:R-HSA-9817362" }, { "val" : "Reactome:R-HSA-983140" }, { "val" : "Reactome:R-HSA-983153" }, { "val" : "Reactome:R-HSA-983156" } ] } }, { "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 process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." }, "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological process" }, { "pred" : "hasExactSynonym", "val" : "physiological process" }, { "pred" : "hasRelatedSynonym", "val" : "single organism process" }, { "pred" : "hasRelatedSynonym", "val" : "single-organism process" } ], "xrefs" : [ { "val" : "Wikipedia:Biological_process" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "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" }, { "val" : "Reactome:R-HSA-6788867" } ] } }, { "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" }, { "val" : "Reactome:R-HSA-162914" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "example to be eventually removed" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000027", "lbl" : "data item", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data item" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000030", "lbl" : "information content entity", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "information content entity" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000102", "lbl" : "data about an ontology part", "meta" : { "definition" : { "val" : "Data about an ontology part is a data item about a part of an ontology, for example a term" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data about an ontology part" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000103", "lbl" : "failed exploratory term", "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "failed exploratory term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000111", "lbl" : "editor preferred term", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "editor preferred term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000112", "lbl" : "example of usage", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "example of usage" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000113", "lbl" : "in branch", "meta" : { "definition" : { "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "in branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP:OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000277" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000114", "lbl" : "has curation status", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has curation status" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Bill Bug" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "lbl" : "definition", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "definition" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000116", "lbl" : "editor note", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "editor note" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000117", "lbl" : "term editor", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term editor" }, { "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" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000118", "lbl" : "alternative label", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like." }, "comments" : [ "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related)." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "alternative label" }, { "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" : "OBO Operations committee" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000119", "lbl" : "definition source", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "definition source" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", "lbl" : "metadata complete", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "metadata complete" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", "lbl" : "organizational term", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "organizational term" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", "lbl" : "ready for release", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ready for release" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", "lbl" : "metadata incomplete", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "metadata incomplete" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", "lbl" : "uncurated", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "uncurated" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000224", "lbl" : "obsolete_core", "meta" : { "definition" : { "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000225", "lbl" : "obsolescence reason specification", "meta" : { "definition" : { "val" : "The reason for which a term has been deprecated. 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" : "obsolescence reason 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" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "placeholder removed" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "terms merged" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000228", "lbl" : "term imported", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term imported" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000229", "lbl" : "term split", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term split" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000231", "lbl" : "has obsolescence reason", "meta" : { "definition" : { "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has obsolescence reason" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000232", "lbl" : "curator note", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An administrative note of use for a curator but of no use for a user" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "curator note" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", "lbl" : "term tracker item", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An IRI or similar locator for a request or discussion of an ontology term." }, "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term tracker item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" }, { "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" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000234", "lbl" : "ontology term requester", "meta" : { "definition" : { "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition." }, "comments" : [ "The 'term requester' can credit the person, organization or project who request the ontology term." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ontology term requester" }, { "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" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000409", "lbl" : "denotator type", "meta" : { "definition" : { "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "denotator type" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Barry Smith, Werner Ceusters" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000410", "lbl" : "universal", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "universal" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000411", "lbl" : "is denotator type", "meta" : { "definition" : { "val" : "Relates an class defined in an ontology, to the type of it's denotator" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is denotator type" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000412", "lbl" : "imported from", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "For external terms/classes, the ontology from which the term was imported" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "imported from" }, { "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" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000420", "lbl" : "defined class", "meta" : { "definition" : { "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "defined class" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000421", "lbl" : "named class expression", "meta" : { "definition" : { "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "named class expression" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000423", "lbl" : "to be replaced with external ontology term", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "to be replaced with external ontology term" }, { "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/IAO_0000424", "lbl" : "expand expression to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "expand expression to" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000425", "lbl" : "expand assertion to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "expand assertion to" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000426", "lbl" : "first order logic expression", "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "first order logic expression" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000427", "lbl" : "antisymmetric property", "meta" : { "definition" : { "val" : "Use boolean value xsd:true to indicate that the property is an antisymmetric property" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "antisymmetric property" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "part_of antisymmetric property xsd:true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000589", "lbl" : "OBO foundry unique label", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An alternative name for a class or property which is unique across the OBO Foundry." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "OBO foundry unique label" }, { "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" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBO Foundry " } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000596", "lbl" : "has ID digit count", "meta" : { "definition" : { "val" : "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has ID digit count" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000597", "lbl" : "has ID range allocated to", "meta" : { "definition" : { "val" : "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has ID range allocated" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000598", "lbl" : "has ID policy for", "meta" : { "definition" : { "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has ID policy for" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000599", "lbl" : "has ID prefix", "meta" : { "definition" : { "val" : "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has ID prefix" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000600", "lbl" : "elucidation", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "elucidation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Barry Smith" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000601", "lbl" : "has associated axiom(nl)", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has associated axiom(nl)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An axiom associated with a term expressed using natural language" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000602", "lbl" : "has associated axiom(fol)", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has associated axiom(fol)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An axiom expressed in first order logic using CLIF syntax" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000603", "lbl" : "is allocated id range", "meta" : { "definition" : { "val" : "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\"" }, "comments" : [ "Add as annotation triples in the granting ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is allocated id range" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000700", "lbl" : "has ontology root term", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has ontology root term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Nicolas Matentzoglu" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0006011", "lbl" : "may be identical to", "meta" : { "definition" : { "val" : "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged." }, "comments" : [ "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "may be identical to" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0006012", "lbl" : "scheduled for obsoletion on or after", "meta" : { "definition" : { "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "scheduled for obsoletion on or after" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall, Jie Zheng" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0010000", "lbl" : "has axiom label", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has axiom id" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0100001", "lbl" : "term replaced by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, "comments" : [ "Add as annotation triples in the granting ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term replaced by" }, { "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" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000000", "lbl" : "ontology module", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ontology file" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000001", "lbl" : "base ontology module", "meta" : { "definition" : { "val" : "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "base ontology module" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000002", "lbl" : "editors ontology module", "meta" : { "definition" : { "val" : "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "editors ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "source ontology module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000003", "lbl" : "main release ontology module", "meta" : { "definition" : { "val" : "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "main release ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000004", "lbl" : "bridge ontology module", "meta" : { "definition" : { "val" : "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "bridge ontology module" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000005", "lbl" : "import ontology module", "meta" : { "definition" : { "val" : "A subset ontology module that is intended to be imported from another ontology." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "import ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: add axioms that indicate this is the output of a module extraction process." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "import file" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://robot.obolibrary.org/extract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000006", "lbl" : "subset ontology module", "meta" : { "definition" : { "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "subset ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ontology slim" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "subset ontology" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://robot.obolibrary.org/filter" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000007", "lbl" : "curation subset ontology module", "meta" : { "definition" : { "val" : "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "curation subset ontology module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000008", "lbl" : "analysis subset ontology module", "meta" : { "definition" : { "val" : "An ontology module that is intended for usage in analysis or discovery applications." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "analysis ontology module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000009", "lbl" : "single layer subset ontology module", "meta" : { "definition" : { "val" : "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "single layer ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ribbon subset" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000010", "lbl" : "exclusion subset ontology module", "meta" : { "definition" : { "val" : "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "exclusion subset ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "antislim" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000011", "lbl" : "external import ontology module", "meta" : { "definition" : { "val" : "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "external import ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "external import" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000012", "lbl" : "species subset ontology module", "meta" : { "definition" : { "val" : "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "species subset ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "taxon subset" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000013", "lbl" : "reasoned ontology module", "meta" : { "definition" : { "val" : "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "reasoned ontology module" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://robot.obolibrary.org/reason" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000014", "lbl" : "generated ontology module", "meta" : { "definition" : { "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "generated ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000015", "lbl" : "template generated ontology module", "meta" : { "definition" : { "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "template generated ontology module" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://robot.obolibrary.org/template" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://doi.org/10.1186/s13326-017-0126-0" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000016", "lbl" : "taxonomic bridge ontology module", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "taxonomic bridge ontology module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000017", "lbl" : "ontology module subsetted by expressivity", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ontology module subsetted by expressivity" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000018", "lbl" : "obo basic subset ontology module", "meta" : { "definition" : { "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obo basic subset ontology module" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000019", "lbl" : "ontology module subsetted by OWL profile", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ontology module subsetted by OWL profile" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000020", "lbl" : "EL++ ontology module", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "EL++ ontology module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000047", "lbl" : "processed material", "type" : "CLASS", "meta" : { "definition" : { "val" : "Is a material entity that is created or changed during material processing." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "processed material" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000967", "lbl" : "container", "type" : "CLASS", "meta" : { "definition" : { "val" : "A device that can be used to restrict the location of material entities over time" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "container" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000968", "lbl" : "device", "type" : "CLASS", "meta" : { "definition" : { "val" : "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "device" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A voltmeter is a measurement device which is intended to perform some measure function." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Helen Parkinson" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "instrument" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI development call 2012-12-17." } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0100026", "lbl" : "organism", "type" : "CLASS", "meta" : { "definition" : { "val" : "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "animal" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "fungus" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "plant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "virus" }, { "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" : "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP: OBI Biomaterial Branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://en.wikipedia.org/wiki/Organism" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OGMS_0000031", "lbl" : "disease", "type" : "CLASS", "meta" : { "definition" : { "val" : "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." } } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0001000", "lbl" : "out of scope", "meta" : { "definition" : { "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0001001", "lbl" : "logical characteristic of object property", "meta" : { "definition" : { "val" : "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBO Operations call" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0002000", "lbl" : "defined by construct", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some (\n and some (\n and some ?Y)))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002103", "lbl" : "synapsed by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002104", "lbl" : "has plasma membrane part", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" }, { "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" : "https://orcid.org/0000-0001-9990-8331" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-1617-8244" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002105", "lbl" : "synapsed_via_type_Ib_bouton_to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton." }, "comments" : [ "Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "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" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002106", "lbl" : "synapsed_via_type_Is_bouton_to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." }, "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "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" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002107", "lbl" : "synapsed_via_type_II_bouton_to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." }, "comments" : [ "Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "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" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002108", "lbl" : "synapsed_by_via_type_II_bouton", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between a muscle and a motor neuron that synapses to it via a type II bouton." }, "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "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" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002109", "lbl" : "synapsed_by_via_type_Ib_bouton", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton." }, "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "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" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002110", "lbl" : "has postsynaptic terminal in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "synapsed in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002111", "lbl" : "releases neurotransmitter", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has neurotransmitter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002112", "lbl" : "synapsed_by_via_type_Is_bouton", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Is bouton." }, "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "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" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002113", "lbl" : "has presynaptic terminal in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "synapses in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some ( that some Y?)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002114", "lbl" : "synapsed_via_type_III_bouton_to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." }, "comments" : [ "Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002115", "lbl" : "synapsed_by_via_type_III_bouton", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between a muscle and a motor neuron that synapses to it via a type III bouton.\n" }, "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002120", "lbl" : "synapsed to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " }, "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002121", "lbl" : "dendrite synapsed in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n\t" }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some (\n\t and some (\n\t http://purl.obolibrary.org/obo/GO_0042734 and some (\n\t and some ?Y)))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002130", "lbl" : "has synaptic terminal in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, "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" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has synapse in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002131", "lbl" : "overlaps", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "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_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002132", "lbl" : "has fasciculating neuron projection", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." }, "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" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has fasciculating component" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002134", "lbl" : "innervates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, "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" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002150", "lbl" : "continuous with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, "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" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "connected to" }, { "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://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002151", "lbl" : "partially overlaps", "type" : "PROPERTY", "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" }, "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_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_0000118", "val" : "proper overlaps" }, { "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/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002156", "lbl" : "derived by descent from", "type" : "PROPERTY", "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ancestral_stucture_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "evolutionarily_descended_from" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002157", "lbl" : "has derived by descendant", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of derived by descent from" }, "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" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002158", "lbl" : "shares ancestor with", "type" : "PROPERTY", "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." }, "comments" : [ "VBO calls this homologous_to" ], "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" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002159", "lbl" : "serially homologous to", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002160", "lbl" : "only in taxon", "type" : "PROPERTY", "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" }, { "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" : "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_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/17921072" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002161", "lbl" : "never in taxon", "type" : "PROPERTY", "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." }, "basicPropertyValues" : [ { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" }, { "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" : "Class: ?X DisjointWith: RO_0002162 some ?Y " }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002162", "lbl" : "in taxon", "type" : "PROPERTY", "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." }, "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" : "https://orcid.org/0000-0001-9227-417X" }, { "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/17921072" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002163", "lbl" : "spatially disjoint from", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" }, "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_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_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" }, { "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_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://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002170", "lbl" : "connected to", "type" : "PROPERTY", "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" }, "basicPropertyValues" : [ { "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)." }, { "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/Connectivity-Design-Pattern" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002171", "lbl" : "mutually spatially disjoint with", "type" : "PROPERTY", "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "non-overlapping with" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "shares no parts with" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX owl: \nPREFIX part_of: \nPREFIX mutually_spatially_disjoint_with: \nCONSTRUCT {\n part_of: a owl:ObjectProperty .\n [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?x ;\n owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?y\n ]\n ]\n}\nWHERE {\n ?x mutually_spatially_disjoint_with: ?y .\n}" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/RO_0002163" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002172", "lbl" : "taxonomic class assertion", "type" : "PROPERTY", "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." }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002173", "lbl" : "ambiguous for taxon", "type" : "PROPERTY", "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]" }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002174", "lbl" : "dubious for taxon", "type" : "PROPERTY", "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." }, "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_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" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", "lbl" : "present in taxon", "type" : "PROPERTY", "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" }, "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { "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" }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002176", "lbl" : "connects", "type" : "PROPERTY", "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The M8 connects Glasgow and Edinburgh" }, { "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)." }, { "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/Connectivity-Design-Pattern" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002177", "lbl" : "attached to part of", "type" : "PROPERTY", "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "attached to part of (anatomical structure to anatomical structure)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", "lbl" : "supplies", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, "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" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002179", "lbl" : "drains", "type" : "PROPERTY", "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." }, "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" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002180", "lbl" : "has component", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "w 'has component' p if 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." }, "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_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." }, { "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" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002200", "lbl" : "has phenotype", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002201", "lbl" : "phenotype of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of has phenotype" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002202", "lbl" : "develops from", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, "comments" : [ "This is the transitive form of the develops from relation" ], "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" : "https://orcid.org/0000-0001-9114-8737" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-1980-3228" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002203", "lbl" : "develops into", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of develops from" }, "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-1980-3228" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002204", "lbl" : "gene product of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" }, "basicPropertyValues" : [ { "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" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002205", "lbl" : "has gene product", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" }, { "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002206", "lbl" : "expressed in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" }, { "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002207", "lbl" : "directly develops from", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." }, "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has developmental precursor" } ], "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "FBbt" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002202" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002208", "lbl" : "parasitoid of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A parasite that kills or sterilizes its host" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002209", "lbl" : "has parasitoid", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of parasitoid of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002210", "lbl" : "directly develops into", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of directly develops from" }, "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "developmental precursor of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", "lbl" : "regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, "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_0000117", "val" : "https://orcid.org/0000-0001-7476-6306" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-3837-8864" }, { "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://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GO" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "regulates (processual)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "false" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002212", "lbl" : "negatively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, "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_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "negatively regulates (process to process)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002213", "lbl" : "positively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, "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_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "positively regulates (process to process)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002214", "lbl" : "has prototype", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" }, { "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" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: add homeomorphy axiom" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002215", "lbl" : "capable of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function realized in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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)\"." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002216", "lbl" : "capable of part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002217", "lbl" : "obsolete actively participates in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" }, "comments" : [ "Obsoleted as the inverse property was obsoleted." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "agent in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002608" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002218", "lbl" : "obsolete has active participant", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has agent" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002500" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002219", "lbl" : "surrounded by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002220", "lbl" : "adjacent to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x adjacent to y if and only if x and y share a boundary." }, "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_0000112", "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." }, { "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 acts as a join point with BSPO" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002221", "lbl" : "surrounds", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of surrounded by" }, "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002222", "lbl" : "temporally related to", "type" : "PROPERTY", "meta" : { "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." }, { "pred" : "http://purl.org/dc/terms/source", "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", "lbl" : "starts", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of starts with" }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Allen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002224", "lbl" : "starts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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_0000112", "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" }, { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "started by" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002225", "lbl" : "develops from part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002226", "lbl" : "develops in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x develops_in y if x is located in y whilst x is developing" }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "EHDAA2" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Jonathan Bard, EHDAA2" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002227", "lbl" : "obligate parasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002228", "lbl" : "facultative parasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002229", "lbl" : "ends", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of ends with" }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002230", "lbl" : "ends with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "finished by" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002231", "lbl" : "has start location", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "starts with process that occurs in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002232", "lbl" : "has end location", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ends with process that occurs in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002233", "lbl" : "has input", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." }, "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", "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "consumes" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002234", "lbl" : "has output", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." }, "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", "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "produces" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002235", "lbl" : "stem parasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002236", "lbl" : "root parasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002237", "lbl" : "hemiparasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002238", "lbl" : "has component participant", "type" : "PROPERTY", "meta" : { "definition" : { "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'." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002240", "lbl" : "has exposure receptor", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000001" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002241", "lbl" : "has exposure stressor", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000000" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002242", "lbl" : "has exposure route", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000055" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002243", "lbl" : "has exposure transport path", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ExO_0000004" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002244", "lbl" : "related via exposure to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Any relationship between an exposure event or process and any other entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002245", "lbl" : "over-expressed in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002246", "lbl" : "under-expressed in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002248", "lbl" : "has active ingredient", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has active substance" }, { "pred" : "hasRelatedSynonym", "val" : "has active pharmaceutical ingredient" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Any portion of roundup 'has active ingredient' some glyphosate" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002249", "lbl" : "active ingredient in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of has active ingredient" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002252", "lbl" : "connecting branch of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004036", "val" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002253", "lbl" : "has connecting branch", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of connecting branch of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004036", "val" : "http://purl.obolibrary.org/obo/BFO_0000051" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002254", "lbl" : "has developmental contribution from", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" }, { "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002255", "lbl" : "developmentally contributes to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of has developmental contribution from" }, "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002256", "lbl" : "developmentally induced by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" }, "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" : "https://orcid.org/0000-0001-9114-8737" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "induced by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GO:0001759" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002257", "lbl" : "developmentally induces", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of developmentally induced by" }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002258", "lbl" : "developmentally preceded by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { "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" : "false" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002259", "lbl" : "defined by inverse", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002260", "lbl" : "has biological role", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002261", "lbl" : "has application role", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002262", "lbl" : "has chemical role", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002263", "lbl" : "acts upstream of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002264", "lbl" : "acts upstream of or within", "type" : "PROPERTY", "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "affects" } ], "basicPropertyValues" : [ { "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." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002285", "lbl" : "developmentally replaces", "type" : "PROPERTY", "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" }, "basicPropertyValues" : [ { "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "replaces" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002286", "lbl" : "developmentally succeeded by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of developmentally preceded by" }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002287", "lbl" : "part of developmental precursor of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" }, { "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002291", "lbl" : "ubiquitously expressed in", "type" : "PROPERTY", "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" }, "basicPropertyValues" : [ { "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" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002293", "lbl" : "ubiquitously expresses", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of ubiquiotously expressed in" }, "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002295", "lbl" : "results in developmental progression of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity 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)." }, "basicPropertyValues" : [ { "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 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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002296", "lbl" : "results in development of", "type" : "PROPERTY", "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." }, "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_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_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.geneontology.org/GO.doc.development.shtml" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "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://purl.obolibrary.org/obo/IAO_0000112", "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" }, { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GOC:mtg_berkeley_2013" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002298", "lbl" : "results in morphogenesis of", "type" : "PROPERTY", "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." }, "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_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_0000112", "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" }, { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GOC:mtg_berkeley_2013" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002299", "lbl" : "results in maturation of", "type" : "PROPERTY", "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." }, "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_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_0000112", "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" }, { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GOC:mtg_berkeley_2013" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002300", "lbl" : "results in disappearance of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" }, { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "May be merged into parent relation" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002301", "lbl" : "results in developmental regression of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" }, { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "May be merged into parent relation" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002302", "lbl" : "is treated by substance", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of 'is substance that treats'" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002303", "lbl" : "has habitat", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." }, "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" }, { "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" : "https://orcid.org/0000-0002-4366-3088" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "adapted for living in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002304", "lbl" : "causally upstream of, positive effect", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." }, "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002411" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002305", "lbl" : "causally upstream of, negative effect", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002309", "lbl" : "has exposure stimulus", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-6996-0040" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-8461-9745" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-06-05T17:35:04Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002310", "lbl" : "obsolete exposure event or process", "type" : "CLASS", "meta" : { "definition" : { "val" : "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-06-05T17:55:39Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002312", "lbl" : "evolutionary variant of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002313", "lbl" : "transports or maintains localization of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." }, "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_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "regulates localization of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002314", "lbl" : "characteristic of part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "inheres in part of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" }, { "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" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002315", "lbl" : "results in acquisition of features of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" }, "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_0000112", "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." }, { "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" : "GOC:mtg_berkeley_2013" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002320", "lbl" : "evolutionarily related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds via some environmental process" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002321", "lbl" : "ecologically related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002322", "lbl" : "confers advantage in", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "adapted for" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002323", "lbl" : "mereotopologically related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A mereological relationship or a topological relationship" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002324", "lbl" : "developmentally related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002325", "lbl" : "colocalizes with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002326", "lbl" : "contributes to", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Contributes_to" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", "lbl" : "enables", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c enables p iff c is capable of p and c acts to execute p." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "catalyzes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is catalyzing" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is executing" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enables" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002328", "lbl" : "functionally related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002329", "lbl" : "part of structure that is capable of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "false" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002330", "lbl" : "genomically related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002331", "lbl" : "involved in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "actively involved in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "enables part of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002332", "lbl" : "regulates levels of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" }, { "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://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "regulates levels of (process to entity)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002333", "lbl" : "enabled by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of enables" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002334", "lbl" : "regulated by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of regulates" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "regulated by (processual)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002335", "lbl" : "negatively regulated by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of negatively regulates" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002336", "lbl" : "positively regulated by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of positively regulates" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002337", "lbl" : "related via localization to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds via some process of localization" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is a grouping relation." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", "lbl" : "has target start location", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." }, "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_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002339", "lbl" : "has target end location", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." }, "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_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002340", "lbl" : "imports", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002341", "lbl" : "results in transport along", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002342", "lbl" : "results in transport across", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002343", "lbl" : "results in growth of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002344", "lbl" : "results in transport to from or in", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002345", "lbl" : "exports", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002348", "lbl" : "results in commitment to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." }, "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_0000112", "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002349", "lbl" : "results in determination of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. 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Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " }, "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_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002357", "lbl" : "results in developmental induction of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002360", "lbl" : "has dendrite location", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/dc/terms/source", "val" : "http://neurolex.org/wiki/Property:DendriteLocation" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002371", "lbl" : "attached to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "attached to (anatomical structure to anatomical structure)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002372", "lbl" : "has muscle origin", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." }, "basicPropertyValues" : [ { "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" : "Wikipedia:Insertion_(anatomy)" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/origin" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002373", "lbl" : "has muscle insertion", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, "basicPropertyValues" : [ { "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" : "Wikipedia:Insertion_(anatomy)" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/insertion" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002374", "lbl" : "derived from ancestral fusion of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" }, "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "has fused element" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "false" }, { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002375", "lbl" : "in branching relationship with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004036", "val" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/170" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002376", "lbl" : "tributary of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. 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It is unlikely to be used in many practical scenarios" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002380", "lbl" : "branching part of", "type" : "PROPERTY", "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" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. 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If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." }, { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002382", "lbl" : "proper distributary of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" }, "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_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002383", "lbl" : "proper tributary of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" }, "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_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002384", "lbl" : "has developmental potential involving", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", "lbl" : "has potential to developmentally contribute to", "type" : "PROPERTY", "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" }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002386", "lbl" : "has potential to developmentally induce", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", "lbl" : "has potential to develop into", "type" : "PROPERTY", "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" }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", "lbl" : "has potential to directly develop into", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002400", "lbl" : "has direct input", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" }, { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly consumes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002401", "lbl" : "obsolete has indirect input", "type" : "PROPERTY", "meta" : { "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], "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" : "https://orcid.org/0000-0002-6601-2165" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002402", "lbl" : "obsolete has direct output", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "translation SubClassOf has_direct_output some protein" }, { "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly produces" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002403", "lbl" : "obsolete has indirect output", "type" : "PROPERTY", "meta" : { "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], "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" : "https://orcid.org/0000-0002-6601-2165" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002404", "lbl" : "causally downstream of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of upstream of" }, "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002405", "lbl" : "immediately causally downstream of", "type" : "PROPERTY", "meta" : { "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002406", "lbl" : "obsolete directly activates", "type" : "PROPERTY", "meta" : { "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002629" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002407", "lbl" : "indirectly positively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "indirectly activates" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002213" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002408", "lbl" : "obsolete directly inhibits", "type" : "PROPERTY", "meta" : { "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002630" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002409", "lbl" : "indirectly negatively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "indirectly inhibits" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002212" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002410", "lbl" : "causally related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002411", "lbl" : "causally upstream of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002412", "lbl" : "immediately causally upstream of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002411" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002413", "lbl" : "provides input for", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly provides input for" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly provides input for (process to process)" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Provides_input_for" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002414", "lbl" : "transitively provides input for", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "transitive form of directly_provides_input_for" }, "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" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "transitively provides input for (process to process)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002416", "lbl" : "logical macro assertion", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002418", "lbl" : "causally upstream of or within", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "affects" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "influences (processual)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002419", "lbl" : "annotation property cardinality", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002420", "lbl" : "logical macro assertion on a class", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A logical macro assertion whose domain is an IRI for a class" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002421", "lbl" : "logical macro assertion on a property", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A logical macro assertion whose domain is an IRI for a property" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002422", "lbl" : "logical macro assertion on an object property", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002423", "lbl" : "logical macro assertion on an annotation property", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002424", "lbl" : "differs in", "type" : "PROPERTY", "meta" : { "comments" : [ "This is an exploratory relation" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002425", "lbl" : "differs in attribute of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002426", "lbl" : "differs in attribute", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002427", "lbl" : "causally downstream of or within", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of causally upstream of or within" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "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://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002428", "lbl" : "involved in regulation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", "lbl" : "involved in positive regulation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002430", "lbl" : "involved in negative regulation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002431", "lbl" : "involved in or involved in regulation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "involved in or reguates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002432", "lbl" : "is active in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "enables activity in" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A protein that enables activity in a cytosol." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes activity in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002433", "lbl" : "contributes to morphology of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", "lbl" : "interacts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "in pairwise interaction with" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Considering relabeling as 'pairwise interacts with'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" }, { "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002435", "lbl" : "genetically interacts with", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000316" }, { "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", "val" : "http://purl.obolibrary.org/obo/MI_0208" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002436", "lbl" : "molecularly interacts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "binds" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "molecularly binds with" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" }, { "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002437", "lbl" : "biotically interacts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "interacts with on organism level" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/interactsWith" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002438", "lbl" : "trophically interacts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship in which the partners are related via a feeding relationship." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002439", "lbl" : "preys on", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Baleen whale preys on krill" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0001-7134-3324" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-3138-4118" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is subject of predation interaction with" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preys upon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/preysUpon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.inaturalist.org/observations/2942824" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002440", "lbl" : "symbiotically interacts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A biotic interaction in which the two organisms live together in more or less intimate association." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "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/19278549" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002441", "lbl" : "commensually interacts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "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/19278549" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002442", "lbl" : "mutualistically interacts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "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/19278549" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002443", "lbl" : "interacts with via parasite-host interaction", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "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/19278549" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002444", "lbl" : "parasite of", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "direct parasite of" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Pediculus humanus capitis parasite of human" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "parasitizes" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/parasitizes" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002445", "lbl" : "parasitized by", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "directly parasitized by" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has parasite" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "parasitised by" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/hasParasite" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002446", "lbl" : "participates in a abiotic-biotic interaction with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "semibiotically interacts with" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Porifiera attaches to substrate" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002447", "lbl" : "phosphorylates", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002448", "lbl" : "directly regulates activity of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly controls" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002449", "lbl" : "directly negatively regulates activity of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly decreases activity of" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-4639-4431" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly inhibits" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002450", "lbl" : "directly positively regulates activity of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly increases activity of" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-4639-4431" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly activates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002451", "lbl" : "transmitted by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between a disease and organism" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "all dengue disease transmitted by some mosquito" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Add domain and range constraints" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002452", "lbl" : "has symptom", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation that holds between a disease or an organism and a phenotype" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002453", "lbl" : "host of", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002454", "lbl" : "has host", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/hasHost" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002455", "lbl" : "pollinates", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Bees pollinate Flowers" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is subject of pollination interaction with" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/pollinates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002456", "lbl" : "pollinated by", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has polinator" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is target of pollination interaction with" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/hasPollinator" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002457", "lbl" : "acquires nutrients from", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002458", "lbl" : "preyed upon by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of preys on" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has predator" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is target of predation interaction with" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/HasPredator" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002459", "lbl" : "is vector for", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Anopheles is a vector for Plasmodium" }, { "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" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002460", "lbl" : "has vector", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002461", "lbl" : "partner in", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002462", "lbl" : "subject participant in", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002463", "lbl" : "target participant in", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002465", "lbl" : "is symbiosis", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002466", "lbl" : "is commensalism", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002467", "lbl" : "is mutualism", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002468", "lbl" : "is parasitism", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002469", "lbl" : "provides nutrients for", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002470", "lbl" : "eats", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is subject of eating interaction with" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002471", "lbl" : "is eaten by", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "eaten by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is target of eating interaction with" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002472", "lbl" : "is evidence for", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002473", "lbl" : "composed primarily of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" }, { "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" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002474", "lbl" : "dispositional interpretation", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002475", "lbl" : "has no connections with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "shares no connection with" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002476", "lbl" : "child nucleus of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002477", "lbl" : "child nucleus of in hermaphrodite", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002478", "lbl" : "child nucleus of in male", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A child nucleus relationship in which the cells are part of a male organism" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002479", "lbl" : "has part that occurs in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002480", "lbl" : "ubiquitinates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002481", "lbl" : "is kinase activity", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002482", "lbl" : "is ubiquitination", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002483", "lbl" : "inherited annotation property", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002484", "lbl" : "curator guidance link", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002485", "lbl" : "receives input from", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "See notes for inverse relation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002486", "lbl" : "sends output to", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002487", "lbl" : "relation between physical entity and a process or stage", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002488", "lbl" : "existence starts during", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002489", "lbl" : "existence starts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002490", "lbl" : "existence overlaps", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", "lbl" : "existence starts and ends during", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" }, "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "exists during" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002492", "lbl" : "existence ends during", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002493", "lbl" : "existence ends with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002494", "lbl" : "transformation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", "lbl" : "immediate transformation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002494" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002496", "lbl" : "existence starts during or after", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", "lbl" : "existence ends during or before", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", "lbl" : "causal agent in process", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002501", "lbl" : "causal relation between processes", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." }, "basicPropertyValues" : [ { "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://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002502", "lbl" : "depends on", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002503", "lbl" : "towards", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." }, { "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/20064205" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002504", "lbl" : "always present in taxon", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "brain always_present_in_taxon 'Vertebrata'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "forelimb always_present_in_taxon Euarchontoglires" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "never lost in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002505", "lbl" : "has intermediate", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has intermediate product" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002506", "lbl" : "causal relation between entities", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" }, { "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://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002507", "lbl" : "determined by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A coral reef environment is determined by a particular coral reef" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" }, { "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/24330602" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "determined by (system to material entity)" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-4366-3088" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002508", "lbl" : "determines", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of determined by" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "determines (material entity to system)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002509", "lbl" : "determined by part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002510", "lbl" : "transcribed from", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is transcribed from y if and only if x is synthesized from template y" }, "basicPropertyValues" : [ { "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/20226267" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002511", "lbl" : "transcribed to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of transcribed from" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "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/20226267" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002512", "lbl" : "ribosomal translation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" }, "basicPropertyValues" : [ { "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/20226267" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002513", "lbl" : "ribosomally translates to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of ribosomal translation of" }, "basicPropertyValues" : [ { "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/20226267" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002514", "lbl" : "sequentially related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. " }, "basicPropertyValues" : [ { "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/20226267" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002515", "lbl" : "sequentially adjacent to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Every UTR is adjacent to a CDS of the same transcript" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Two consecutive DNA residues are sequentially adjacent" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" }, { "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/20226267" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002516", "lbl" : "has start sequence", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Every CDS has as a start sequence the start codon for that transcript" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "started by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002517", "lbl" : "is start sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of has start sequence" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "starts" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002518", "lbl" : "has end sequence", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ended by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002519", "lbl" : "is end sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of has end sequence" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ends" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002520", "lbl" : "is consecutive sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "In the SO paper, this was defined as an instance-type relation" }, { "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/20226267" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002521", "lbl" : "is sequentially aligned with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002522", "lbl" : "bounds sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002523", "lbl" : "is bound by sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of bounds sequence of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002524", "lbl" : "has subsequence", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "contains" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002525", "lbl" : "is subsequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of has subsequence" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "contained by" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002526", "lbl" : "overlaps sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002527", "lbl" : "does not overlap sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "disconnected from" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002528", "lbl" : "is upstream of sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of downstream of sequence of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002529", "lbl" : "is downstream of sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002530", "lbl" : "is immediately downstream of sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002529" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002531", "lbl" : "is immediately upstream of sequence of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of immediately downstream of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002532", "lbl" : "sequentially ordered entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "Any entity that is ordered in discrete units along a linear axis." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002533", "lbl" : "sequence atomic unit", "type" : "CLASS", "meta" : { "definition" : { "val" : "Any individual unit of a collection of like units arranged in a linear order" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002534", "lbl" : "sequence bearer", "type" : "CLASS", "meta" : { "definition" : { "val" : "Any entity that can be divided into parts such that each part is an atomical unit of a sequence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002535", "lbl" : "temporal logical macro assertion on a class", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002536", "lbl" : "measurement property has unit", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002537", "lbl" : "has start time value", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002538", "lbl" : "has end time value", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002539", "lbl" : "start, days post fertilization", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property." }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002540", "lbl" : "end, days post fertilization", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property." }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002541", "lbl" : "start, years post birth", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1." }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002542", "lbl" : "end, years post birth", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2" }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002543", "lbl" : "start, months post birth", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1." }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002544", "lbl" : "end, months post birth", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2" }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002545", "lbl" : "month of gestation", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in." }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002546", "lbl" : "has developmental stage marker", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process" }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002547", "lbl" : "start, days post coitum", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Count of number of days intervening between the start of the stage and the time of coitum." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002548", "lbl" : "end, days post coitum", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Count of number of days intervening between the end of the stage and the time of coitum." }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002549", "lbl" : "start, weeks post birth", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002550", "lbl" : "end, weeks post birth", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002551", "lbl" : "has skeleton", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has supporting framework" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002552", "lbl" : "results in ending of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002553", "lbl" : "hyperparasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "hyperparasitoid of" }, { "pred" : "hasRelatedSynonym", "val" : "epiparasite of" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" }, { "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://eol.org/schema/terms/hyperparasitoidOf" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Hyperparasite" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002554", "lbl" : "hyperparasitized by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of hyperparasite of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "has epiparasite" }, { "pred" : "hasRelatedSynonym", "val" : "has hyperparasite" }, { "pred" : "hasRelatedSynonym", "val" : "hyperparasitoidized by" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002555", "lbl" : "allelopath of", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "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://en.wikipedia.org/wiki/Allelopathy" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://eol.org/schema/terms/allelopathyYes" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002556", "lbl" : "pathogen of", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002557", "lbl" : "has pathogen", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002558", "lbl" : "has evidence", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of is evidence for" }, "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "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/25052702" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002559", "lbl" : "causally influenced by", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "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://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "causally influenced by (entity-centric)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002560", "lbl" : "is asymmetric relational form of process class", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p" }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002561", "lbl" : "is symmetric relational form of process class", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p" }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002562", "lbl" : "is relational form of process class", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process" }, "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "lbl" : "interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002564", "lbl" : "molecular interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002565", "lbl" : "results in movement of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" }, "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_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002566", "lbl" : "causally influences", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-4639-4431" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "causally influences (entity-centric)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002567", "lbl" : "biomechanically related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002568", "lbl" : "has muscle antagonist", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." }, "basicPropertyValues" : [ { "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" : "Wikipedia:Antagonist_(muscle)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002569", "lbl" : "has branching part", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of branching part of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002570", "lbl" : "conduit for", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "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" : "UBERON:cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002571", "lbl" : "lumen of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "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" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002572", "lbl" : "luminal space of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002573", "lbl" : "has modifier", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation that holds between an attribute or a qualifier and another attribute." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "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/20064205" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002574", "lbl" : "participates in a biotic-biotic interaction with", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002575", "lbl" : "is direct form of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002423", "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002576", "lbl" : "skeleton of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of has skeleton" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002577", "lbl" : "system", "type" : "CLASS", "meta" : { "definition" : { "val" : "A material entity consisting of multiple components that are causally integrated." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" }, { "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.jbiomedsem.com/content/4/1/43" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002578", "lbl" : "directly regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." }, "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_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly regulates (processual)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002579", "lbl" : "is indirect form of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002580", "lbl" : "logical macro assertion on an axiom", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002581", "lbl" : "is a defining property chain axiom", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002582", "lbl" : "is a defining property chain axiom where second argument is reflexive", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002583", "lbl" : "existence starts at end of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002584", "lbl" : "has part structure that is capable of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002585", "lbl" : "results in closure of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002586", "lbl" : "results in breakdown of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002587", "lbl" : "results in synthesis of", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002588", "lbl" : "results in assembly of", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002589", "lbl" : "results in catabolism of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002590", "lbl" : "results in disassembly of", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002591", "lbl" : "results in remodeling of", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002592", "lbl" : "results in organization of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002593", "lbl" : "existence ends at start of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002594", "lbl" : "is relational form of a class", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002595", "lbl" : "causal relation between material entity and a process", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." }, { "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://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002596", "lbl" : "capable of regulating", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pyrethroid -> growth" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002597", "lbl" : "capable of negatively regulating", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002598", "lbl" : "capable of positively regulating", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "renin -> arteriolar smooth muscle contraction" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002599", "lbl" : "capable of inhibiting or preventing pathological process", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pazopanib -> pathological angiogenesis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "treats" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002600", "lbl" : "capable of upregulating or causing pathological process", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "benzene -> cancer [CHEBI]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "causes disease" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002601", "lbl" : "logical macro assertion involving identity", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A shortcut relationship that holds between two entities based on their identity criteria" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002602", "lbl" : "in approximate one to one relationship with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002603", "lbl" : "is approximately equivalent to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002604", "lbl" : "is opposite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002605", "lbl" : "is indistinguishable from", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002606", "lbl" : "is substance that treats", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "treats" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002607", "lbl" : "is marker for", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "May be ceded to OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002608", "lbl" : "process has causal agent", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of 'causal agent in process'" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002609", "lbl" : "obsolete related via dependence to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002610", "lbl" : "correlated with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Groups both positive and negative correlation" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002611", "lbl" : "evidential logical macro assertion on an axiom", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002612", "lbl" : "axiom has evidence", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002613", "lbl" : "axiom contradicted by evidence", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002614", "lbl" : "is evidence with support from", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." }, "comments" : [ "In the Gene Ontology association model, this corresponds to the With/From field" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002615", "lbl" : "has model", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of is-model-of" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002616", "lbl" : "related via evidence or inference to", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is a grouping relation." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002617", "lbl" : "is representative IRI for equivalence set", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002618", "lbl" : "visits", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/issues/74" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002619", "lbl" : "visited by", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002622", "lbl" : "visits flowers of", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002623", "lbl" : "has flowers visited by", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002624", "lbl" : "lays eggs in", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002625", "lbl" : "has eggs laid in by", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002626", "lbl" : "kills", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://github.com/jhpoelen/eol-globi-data/issues/143" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002627", "lbl" : "is killed by", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002629", "lbl" : "directly positively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." }, "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_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly positively regulates (process to process)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002630", "lbl" : "directly negatively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." }, "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_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly negatively regulates (process to process)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002632", "lbl" : "ectoparasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002633", "lbl" : "has ectoparasite", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of ectoparasite of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002634", "lbl" : "endoparasite of", "type" : "PROPERTY", "meta" : { "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "lives inside of" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002635", "lbl" : "has endoparasite", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002636", "lbl" : "mesoparasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002637", "lbl" : "has mesoparasite", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of mesoparasite of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002638", "lbl" : "intercellular endoparasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002639", "lbl" : "has intercellular endoparasite", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of intercellular endoparasite of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002640", "lbl" : "intracellular endoparasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A sub-relation of endoparasite-of in which the parasite inhabits host cells." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002641", "lbl" : "has intracellular endoparasite", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of intracellular endoparasite of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002801", "lbl" : "co-roosts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002802", "lbl" : "reservoir host of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." }, "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://doi.org/10.3390/v13071356" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-3120-4802" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-3138-4118" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002803", "lbl" : "has reservoir host", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of reservoir host of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", "type" : "PROPERTY", "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." }, "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_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0001-9114-8737" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003001", "lbl" : "produced by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a produced_by b iff some process that occurs_in b has_output a." }, "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" : "https://orcid.org/0000-0001-9114-8737" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003003", "lbl" : "increases expression of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. 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key biological process." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease has basis in disruption of (disease to process)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:37:52Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004022", "lbl" : "disease has basis in feature", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:46:07Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004023", "lbl" : "causal relationship with disease as subject", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:50:54Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004024", "lbl" : "disease causes disruption of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease causes disruption of (disease to process)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:51:09Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004025", "lbl" : "disease causes dysfunction of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease causes dysfunction of (disease to anatomical entity)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:58:20Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004026", "lbl" : "disease has location", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T04:06:02Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004027", "lbl" : "disease has inflammation site", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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" }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:37:31Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004028", "lbl" : "realized in response to stimulus", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:45:49Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004029", "lbl" : "disease has feature", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:50:53Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004030", "lbl" : "disease arises from alteration in structure", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:58:44Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004031", "lbl" : "enables subfunction", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-25T23:20:13Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004032", "lbl" : "acts upstream of or within, positive effect", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002264" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:30Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004033", "lbl" : "acts upstream of or within, negative effect", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002264" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:51Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004034", "lbl" : "acts upstream of, positive effect", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:53:14Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004035", "lbl" : "acts upstream of, negative effect", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:53:22Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004036", "lbl" : "nominally disjoint with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004046", "lbl" : "causally upstream of or within, negative effect", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004047", "lbl" : "causally upstream of or within, positive effect", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002418" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004048", "lbl" : "is directional form of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:59:29Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004049", "lbl" : "is positive form of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:16Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004050", "lbl" : "is negative form of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:24Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004096", "lbl" : "DEPRECATED inheres in", "type" : "PROPERTY", "meta" : { "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004097", "lbl" : "DEPRECATED bearer of", "type" : "PROPERTY", "meta" : { "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0007000", "lbl" : "has driver", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-8910-9851" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/issues/506" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0007001", "lbl" : "has disease driver", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-8910-9851" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/issues/506" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008501", "lbl" : "epiphyte of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Epiphyte" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008502", "lbl" : "has epiphyte", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of epiphyte of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008503", "lbl" : "kleptoparasite of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008504", "lbl" : "kleptoparasitized by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of kleptoparasite of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008505", "lbl" : "creates habitat for", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008506", "lbl" : "ecologically co-occurs with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008507", "lbl" : "lays eggs on", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008508", "lbl" : "has eggs laid on by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of lays eggs on" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008509", "lbl" : "has roost", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." }, "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-2908-3327" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2023-01-18T14:28:21Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009001", "lbl" : "has substance added", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "muffin 'has substance added' some 'baking soda'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-8844-9165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009002", "lbl" : "has substance removed", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'egg white' 'has substance removed' some 'egg yolk'" }, { "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" : "https://orcid.org/0000-0002-8844-9165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009003", "lbl" : "immersed in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "sardines 'immersed in' some 'oil and mustard'" }, { "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" : "https://orcid.org/0000-0002-8844-9165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009004", "lbl" : "has consumer", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "sardine has consumer some homo sapiens" }, { "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" : "https://orcid.org/0000-0002-8844-9165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009005", "lbl" : "has primary substance added", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "'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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "bread 'has primary substance added' some 'flour'" }, { "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" : "https://orcid.org/0000-0002-8844-9165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", 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] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013002", "lbl" : "receives synaptic input in region", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:42:23Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013003", "lbl" : "sends synaptic output to region", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:45:06Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013004", "lbl" : "has synaptic IO throughout", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:52:19Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013005", "lbl" : "receives synaptic input throughout", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:55:36Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013006", "lbl" : "sends synaptic output throughout", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:57:27Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013007", "lbl" : "has sensory dendrite in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has sensory dendrite location" }, { "pred" : "hasExactSynonym", "val" : "has sensory terminal in" }, { "pred" : "hasExactSynonym", "val" : "has sensory terminal location" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013008", "lbl" : "receives synaptic input from neuron", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:40:18Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013009", "lbl" : "sends synaptic output to cell", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." }, "comments" : [ "Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-05-26T08:41:07Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0014001", "lbl" : "disease has infectious agent", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015001", "lbl" : "has exemplar data", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "C 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X != Y; all members of X are also members of Y." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0001-7258-9596" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015004", "lbl" : "has characterizing marker set", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has marker gene combination" }, { "pred" : "hasExactSynonym", "val" : "has marker signature set" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus 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location. In these cases it is recommended to make a more specific cell class restricted to the relevant context." }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-7258-9596" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015006", "lbl" : "different in magnitude relative to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015007", "lbl" : "increased in magnitude relative to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015008", "lbl" : "decreased in magnitude relative to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015009", "lbl" : "similar in magnitude relative to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015010", "lbl" : "has relative magnitude", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0015011", "lbl" : "has cross section", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015012", "lbl" : "reciprocal of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, "comments" : [ "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. 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It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/issues/478" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0016002", "lbl" : "has disease", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/issues/478" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0016004", "lbl" : "has exposure medium", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ExO:0000083" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-7463-6306" }, { 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input." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0017003", "lbl" : "positively correlated with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between entities in which one increases or decreases as the other does the same." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly correlated with" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1909-9269" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0017004", "lbl" : "negatively correlated with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between entities in which one increases as the other decreases." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "inversely correlated with" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1909-9269" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0017005", "lbl" : "contains measured amount", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-2999-0103" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-5714-991X" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", "type" : "PROPERTY", "meta" : { 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