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omo.json
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omo.json
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{
"graphs" : [ {
"id" : "http://purl.obolibrary.org/obo/omo.json",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://protege.stanford.edu/plugins/owl/protege#defaultLanguage",
"val" : "en"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Adam Goldstein"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Alan Ruttenberg"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Albert Goldfain"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Barry Smith"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Bjoern Peters"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Carlo Torniai"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Chris Mungall"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Chris Stoeckert"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Christian A. Boelling"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Darren Natale"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "David Osumi-Sutherland"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Gwen Frishkoff"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Holger Stenzhorn"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "James A. Overton"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "James Malone"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Jennifer Fostel"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Jie Zheng"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Jonathan Rees"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Larisa Soldatova"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Lawrence Hunter"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Matt Brush"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Melanie Courtot"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Michel Dumontier"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Paolo Ciccarese"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Pat Hayes"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Philippe Rocca-Serra"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Randy Dipert"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Ron Rudnicki"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Satya Sahoo"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Sivaram Arabandi"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Werner Ceusters"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "William Duncan"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "William Hogan"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Yongqun (Oliver) He"
}, {
"pred" : "http://purl.org/dc/elements/1.1/description",
"val" : "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)."
}, {
"pred" : "http://purl.org/dc/elements/1.1/title",
"val" : "OBO Metadata Ontology"
}, {
"pred" : "http://purl.org/dc/terms/license",
"val" : "https://creativecommons.org/publicdomain/zero/1.0/"
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2023-11-02"
} ],
"version" : "http://purl.obolibrary.org/obo/omo/releases/2023-11-02/omo.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:<http://purl.obolibrary.org/obo/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/OMO_0001002",
"lbl" : "domain entity does not exist",
"type" : "INDIVIDUAL",
"meta" : {
"definition" : {
"val" : "The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). "
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "http://orcid.org/0000-0002-4142-7153"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
"val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/136"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000234",
"val" : "https://orcid.org/0000-0002-4142-7153"
} ]
}
}, {
"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:<http://purl.obolibrary.org/obo/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:<http://purl.obolibrary.org/obo/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:<http://purl.obolibrary.org/obo/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:<http://purl.obofoundry.org/obo/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:<http://purl.obolibrary.org/obo/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:<http://purl.obolibrary.org/obo/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:<http://purl.obolibrary.org/obo/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:<http://purl.obolibrary.org/obo/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 <http://obofoundry.org/>"
} ]
}
}, {
"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",