{ "graphs" : [ { "id" : "http://purl.obolibrary.org/obo/vbo.json", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000700", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000700", "val" : "http://purl.obolibrary.org/obo/VBO_0300000" }, { "pred" : "http://purl.org/dc/terms/description", "val" : "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names." }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://purl.org/dc/terms/title", "val" : "Vertebrate Breed Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", "val" : "2023-03-09" } ], "version" : "http://purl.obolibrary.org/obo/vbo/releases/2023-03-09/vbo.json" }, "nodes" : [ { "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_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_0000103", "lbl" : "failed exploratory term", "type" : "INDIVIDUAL", "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_0000225", "lbl" : "obsolescence reason specification", "type" : "CLASS", "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_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" } ] } }, { "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_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" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "placeholder removed" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "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", "type" : "INDIVIDUAL", "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", "type" : "INDIVIDUAL", "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_0000410", "lbl" : "universal", "type" : "INDIVIDUAL", "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_0000409", "lbl" : "denotator type", "type" : "CLASS", "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_0000420", "lbl" : "defined class", "type" : "INDIVIDUAL", "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", "type" : "INDIVIDUAL", "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_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_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0001000", "lbl" : "out of scope", "type" : "INDIVIDUAL", "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { "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" : "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" : "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" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." } } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", "lbl" : "role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." } } }, { "id" : "http://purl.obolibrary.org/obo/BFO_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" } ] } }, { "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_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/elements/1.1/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_0000141", "lbl" : "immaterial entity", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/CARO_0010004", "lbl" : "cellular organism", "type" : "CLASS" }, { "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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", "xrefs" : [ "GOC:pdt" ] }, "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecular function" } ] } }, { "id" : "http://purl.obolibrary.org/obo/GO_0008150", "lbl" : "biological_process", "type" : "CLASS", "meta" : { "definition" : { "val" : "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", "xrefs" : [ "GOC:pdt" ] }, "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological process" }, { "pred" : "hasExactSynonym", "val" : "physiological process" }, { "pred" : "hasRelatedSynonym", "val" : "single organism process" }, { "pred" : "hasRelatedSynonym", "val" : "single-organism process" } ], "xrefs" : [ { "val" : "Wikipedia:Biological_process" } ], "basicPropertyValues" : [ { "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/IAO_0000027", "lbl" : "data item", "type" : "CLASS", "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", "type" : "CLASS", "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_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", "type" : "PROPERTY", "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_0000224", "lbl" : "obsolete_core", "type" : "INDIVIDUAL", "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000231", "lbl" : "has obsolescence reason", "type" : "PROPERTY", "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", "type" : "PROPERTY", "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_0000411", "lbl" : "is denotator type", "type" : "PROPERTY", "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_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" : { "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", "type" : "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", "type" : "PROPERTY", "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", "type" : "PROPERTY", "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", "type" : "PROPERTY", "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", "type" : "PROPERTY", "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)", "type" : "PROPERTY", "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)", "type" : "PROPERTY", "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", "type" : "PROPERTY", "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", "type" : "PROPERTY", "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "#40" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "VFB" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0006012", "lbl" : "scheduled for obsoletion on or after", "type" : "PROPERTY", "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/15532" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/32" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "GO ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0010000", "lbl" : "has axiom label", "type" : "PROPERTY", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : "CLASS", "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", "type" : 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