diff --git a/omo-full.json b/omo-full.json index 9943a1c..77045ce 100644 --- a/omo-full.json +++ b/omo-full.json @@ -121,18 +121,28 @@ "val" : "https://creativecommons.org/publicdomain/zero/1.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-11-02" + "val" : "2024-11-13" } ], - "version" : "http://purl.obolibrary.org/obo/omo/releases/2023-11-02/omo-full.json" + "version" : "http://purl.obolibrary.org/obo/omo/releases/2024-11-13/omo-full.json" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_0000027", + "lbl" : "data item", + "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" + "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" } ] } }, { @@ -164,16 +174,16 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "lbl" : "failed exploratory term", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "lbl" : "data about an ontology part", + "type" : "CLASS", "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" + "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" : "failed exploratory term" + "val" : "data about an ontology part" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" @@ -205,532 +215,462 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_0000409", + "lbl" : "denotator type", + "type" : "CLASS", "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." + "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" : "metadata complete" + "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_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000000", + "lbl" : "ontology module", + "type" : "CLASS", "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" + "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_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000001", + "lbl" : "base ontology module", + "type" : "CLASS", "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.\"" + "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" : "ready for release" + "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_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000002", + "lbl" : "editors ontology module", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + "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" : "metadata incomplete" + "val" : "editors ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "source ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000003", + "lbl" : "main release ontology module", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + "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" : "uncurated" + "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_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000004", + "lbl" : "bridge ontology module", + "type" : "CLASS", "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." + "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" : "pending final vetting" + "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_0000226", - "lbl" : "placeholder removed", - "type" : "INDIVIDUAL", + "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" : "placeholder removed" + "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_0000227", - "lbl" : "terms merged", - "type" : "INDIVIDUAL", + "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" : "terms merged" + "val" : "subset ontology module" }, { - "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." + "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_0000228", - "lbl" : "term imported", - "type" : "INDIVIDUAL", + "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" : "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." + "val" : "curation subset ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "lbl" : "term split", - "type" : "INDIVIDUAL", + "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" : "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." + "val" : "analysis ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "lbl" : "universal", - "type" : "INDIVIDUAL", + "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" : "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" + "val" : "single layer ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribbon subset" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000409", - "lbl" : "denotator type", + "id" : "http://purl.obolibrary.org/obo/IAO_8000010", + "lbl" : "exclusion subset ontology module", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective." + "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" : "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" + "val" : "exclusion subset ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Barry Smith, Werner Ceusters" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "antislim" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "lbl" : "defined class", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000011", + "lbl" : "external import ontology module", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" + "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" : "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." + "val" : "external import ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "external import" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "lbl" : "named class expression", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000012", + "lbl" : "species subset ontology module", + "type" : "CLASS", "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." + "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" : "named class expression" + "val" : "species subset ontology module" }, { - "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_0000118", + "val" : "taxon subset" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" + "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_0000423", - "lbl" : "to be replaced with external ontology term", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000013", + "lbl" : "reasoned ontology module", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology." + "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" : "to be replaced with external ontology term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" + "val" : "reasoned ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/reason" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000014", + "lbl" : "generated ontology module", + "type" : "CLASS", "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." + "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" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" + "val" : "generated ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" + "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/OMO_0001000", - "lbl" : "out of scope", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000015", + "lbl" : "template generated ontology module", + "type" : "CLASS", "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." + "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_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_0000111", + "val" : "template generated ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/template" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://doi.org/10.1186/s13326-017-0126-0" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "https://orcid.org/0000-0001-5208-3432" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0001002", - "lbl" : "domain entity does not exist", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000016", + "lbl" : "taxonomic bridge ontology module", + "type" : "CLASS", "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" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "taxonomic bridge ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000027", - "lbl" : "data item", + "id" : "http://purl.obolibrary.org/obo/IAO_8000017", + "lbl" : "ontology module subsetted by expressivity", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data item" + "val" : "ontology module subsetted by expressivity" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000030", - "lbl" : "information content entity", + "id" : "http://purl.obolibrary.org/obo/IAO_8000018", + "lbl" : "obo basic subset ontology module", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "information content entity" + "val" : "obo basic subset ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000102", - "lbl" : "data about an ontology part", + "id" : "http://purl.obolibrary.org/obo/IAO_8000019", + "lbl" : "ontology module subsetted by OWL profile", "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" + "val" : "ontology module subsetted by OWL profile" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000111", - "lbl" : "editor preferred term", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000020", + "lbl" : "EL++ ontology module", + "type" : "CLASS", "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:" + "val" : "EL++ ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000112", - "lbl" : "example of usage", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL", "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:" + "val" : "example to be eventually removed" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000113", - "lbl" : "in branch", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet." + "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" : "in branch" + "val" : "failed exploratory term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "GROUP:OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000277" + "val" : "Person:Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000114", - "lbl" : "has curation status", - "type" : "PROPERTY", + "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" : "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" + "val" : "metadata complete" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", "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." + "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" : "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:" + "val" : "organizational term" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", "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." + "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" : "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:" + "val" : "ready for release" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000117", - "lbl" : "term editor", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", "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" + "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" : "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:" + "val" : "metadata incomplete" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000118", - "lbl" : "alternative label", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", "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." + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." }, - "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:" + "val" : "uncurated" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000119", - "lbl" : "definition source", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", "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" + "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" : "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:" + "val" : "pending final vetting" } ] } }, { @@ -754,833 +694,931 @@ "deprecated" : true } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "lbl" : "has obsolescence reason", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "type" : "INDIVIDUAL", "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" + "val" : "placeholder removed" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000232", - "lbl" : "curator note", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "type" : "INDIVIDUAL", "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" + "val" : "terms merged" }, { - "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" : "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_0000117", - "val" : "PERSON:Alan Ruttenberg" + "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_0000233", - "lbl" : "term tracker item", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "type" : "INDIVIDUAL", "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" + "val" : "term split" }, { - "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_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_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "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" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000234", - "lbl" : "ontology term requester", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition." + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, - "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" + "val" : "defined class" }, { - "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" : "\"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" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + "val" : "Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000411", - "lbl" : "is denotator type", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "Relates an class defined in an ontology, to the type of it's denotator" + "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" : "is denotator type" + "val" : "named class expression" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + "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_0000412", - "lbl" : "imported from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "For external terms/classes, the ontology from which the term was imported" + "val" : "Terms with this status should eventually replaced with a term from another ontology." }, "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" + "val" : "to be replaced with external ontology term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" + "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" + "val" : "group:OBI" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "lbl" : "expand expression to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", "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" + "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" : "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" + "val" : "requires discussion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000425", - "lbl" : "expand assertion to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom." + "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_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_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" : "Chris Mungall" + "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/IAO_0000426", - "lbl" : "first order logic expression", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/OMO_0001002", + "lbl" : "domain entity does not exist", + "type" : "INDIVIDUAL", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "first order logic expression" + "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" : "PERSON:Alan Ruttenberg" + "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_0000427", - "lbl" : "antisymmetric property", + "id" : "http://protege.stanford.edu/plugins/owl/protege#defaultLanguage", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "lbl" : "editor preferred term", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Use boolean value xsd:true to indicate that the property is an antisymmetric property" + "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" : "antisymmetric property" + "val" : "editor preferred term" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "part_of antisymmetric property xsd:true" + "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" : "Alan Ruttenberg" + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000589", - "lbl" : "OBO foundry unique label", + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl" : "example of usage", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An alternative name for a class or property which is unique across the OBO Foundry." + "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" : "OBO foundry unique label" + "val" : "example of usage" }, { "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" + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" + "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBO Foundry " + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000596", - "lbl" : "has ID digit count", + "id" : "http://purl.obolibrary.org/obo/IAO_0000113", + "lbl" : "in branch", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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)" + "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" : "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\"" + "val" : "in branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" + "val" : "GROUP:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000277" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000597", - "lbl" : "has ID range allocated to", + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "lbl" : "has curation status", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" + "val" : "has curation status" }, { - "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000598", - "lbl" : "has ID policy for", + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages" + "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" : "has ID policy for" + "val" : "definition" }, { - "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_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:Alan Ruttenberg" + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000599", - "lbl" : "has ID prefix", + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "has ID prefix" + "val" : "editor note" }, { - "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_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000600", - "lbl" : "elucidation", + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "lbl" : "term editor", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "elucidation" + "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:Alan Ruttenberg" + "val" : "PERSON:Daniel Schober" }, { "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" + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000601", - "lbl" : "has associated axiom(nl)", + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "lbl" : "alternative label", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "has associated axiom(nl)" + "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" : "Person:Alan Ruttenberg" + "val" : "OBO Operations committee" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An axiom associated with a term expressed using natural language" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000602", - "lbl" : "has associated axiom(fol)", + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "lbl" : "definition source", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "has associated axiom(fol)" + "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:Alan Ruttenberg" + "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An axiom expressed in first order logic using CLIF syntax" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000603", - "lbl" : "is allocated id range", + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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\"" + "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." }, - "comments" : [ "Add as annotation triples in the granting ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is allocated id range" + "val" : "has obsolescence reason" }, { "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" + "val" : "PERSON:Melanie Courtot" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0006011", - "lbl" : "may be identical to", + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "lbl" : "curator note", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "val" : "An administrative note of use for a curator but of no use for a user" }, - "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" + "val" : "curator note" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "#40" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "VFB" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0006012", - "lbl" : "scheduled for obsoletion on or after", + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date." + "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" : "scheduled for obsoletion on or after" + "val" : "term tracker item" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall, Jie Zheng" + "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_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/15532" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "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_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "GO ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0010000", - "lbl" : "has axiom label", + "id" : "http://purl.obolibrary.org/obo/IAO_0000234", + "lbl" : "ontology term requester", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "has axiom id" + "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:Alan Ruttenberg" + "val" : "Person: Jie Zheng, Chris Stoeckert, 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" + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", + "id" : "http://purl.obolibrary.org/obo/IAO_0000411", + "lbl" : "is denotator type", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" + "val" : "Relates an class defined in an ontology, to the type of it's denotator" }, - "comments" : [ "Add as annotation triples in the granting ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" + "val" : "is denotator type" }, { - "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" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" + "val" : "Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000000", - "lbl" : "ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000412", + "lbl" : "imported from", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "ontology module" + "val" : "imported from" }, { - "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_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ontology file" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" }, { - "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." + "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_8000001", - "lbl" : "base ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "base ontology module" + "val" : "expand expression to" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" + "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_8000002", - "lbl" : "editors ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000425", + "lbl" : "expand assertion to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "editors ontology module" + "val" : "expand assertion to" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "source ontology module" + "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_8000003", - "lbl" : "main release ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "lbl" : "first order logic expression", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" + "val" : "first order logic expression" }, { - "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" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000004", - "lbl" : "bridge ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000427", + "lbl" : "antisymmetric property", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "bridge ontology module" + "val" : "antisymmetric property" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + "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_8000005", - "lbl" : "import ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl" : "OBO foundry unique label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A subset ontology module that is intended to be imported from another ontology." + "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" : "import ontology module" + "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" : "TODO: add axioms that indicate this is the output of a module extraction process." + "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_0000118", - "val" : "import file" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://robot.obolibrary.org/extract" + "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_8000006", - "lbl" : "subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000596", + "lbl" : "has ID digit count", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." + "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" : "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" + "val" : "has ID digit count" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://robot.obolibrary.org/filter" + "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://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000007", - "lbl" : "curation subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000597", + "lbl" : "has ID range allocated to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "curation subset ontology module" + "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_8000008", - "lbl" : "analysis subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000598", + "lbl" : "has ID policy for", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An ontology module that is intended for usage in analysis or discovery applications." + "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" : "analysis ontology module" + "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_8000009", - "lbl" : "single layer subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000599", + "lbl" : "has ID prefix", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "single layer ontology module" + "val" : "has ID prefix" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ribbon subset" + "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_8000010", - "lbl" : "exclusion subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl" : "elucidation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" + "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_0000118", - "val" : "antislim" + "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_8000011", - "lbl" : "external import ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000601", + "lbl" : "has associated axiom(nl)", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" + "val" : "has associated axiom(nl)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "external import" + "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_8000012", - "lbl" : "species subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000602", + "lbl" : "has associated axiom(fol)", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" + "val" : "has associated axiom(fol)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "taxon subset" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://purl.obolibrary.org/obo/IAO_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_8000013", - "lbl" : "reasoned ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000603", + "lbl" : "is allocated id range", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "reasoned ontology module" + "val" : "is allocated id range" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://robot.obolibrary.org/reason" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000014", - "lbl" : "generated ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "has ontology root term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." + "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" : "generated ontology module" + "val" : "has ontology root term" }, { - "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" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Nicolas Matentzoglu" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000015", - "lbl" : "template generated ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0006011", + "lbl" : "may be identical to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template." + "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" : "template generated ontology module" + "val" : "may be identical to" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://robot.obolibrary.org/template" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://doi.org/10.1186/s13326-017-0126-0" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "#40" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000016", - "lbl" : "taxonomic bridge ontology module", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "taxonomic bridge ontology module" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000017", - "lbl" : "ontology module subsetted by expressivity", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ontology module subsetted by expressivity" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "VFB" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000018", - "lbl" : "obo basic subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0006012", + "lbl" : "scheduled for obsoletion on or after", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" + "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" : "obo basic subset ontology module" + "val" : "scheduled for obsoletion on or after" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + "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_8000019", - "lbl" : "ontology module subsetted by OWL profile", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0010000", + "lbl" : "has axiom label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ontology module subsetted by OWL profile" + "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_8000020", - "lbl" : "EL++ ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "EL++ ontology module" + "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/OMO_0001001", "lbl" : "logical characteristic of object property", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL." @@ -1597,6 +1635,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0002000", "lbl" : "defined by construct", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." @@ -1619,6 +1658,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003000", "lbl" : "abbreviation", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing abbreviations or initalisms" @@ -1641,6 +1681,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003001", "lbl" : "ambiguous synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing ambiguous synonyms" @@ -1660,6 +1701,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003002", "lbl" : "dubious synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing dubious synonyms" @@ -1679,6 +1721,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003003", "lbl" : "layperson synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing layperson or colloquial synonyms" @@ -1701,6 +1744,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003004", "lbl" : "plural form", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing pluralization synonyms" @@ -1723,6 +1767,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003005", "lbl" : "UK spelling synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing UK spelling variants" @@ -1745,6 +1790,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003006", "lbl" : "misspelling", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for common misspellings" @@ -1764,6 +1810,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003007", "lbl" : "misnomer", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway" @@ -1783,6 +1830,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003008", "lbl" : "previous name", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for names that have been used as primary labels in the past." @@ -1805,6 +1853,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003009", "lbl" : "legal name", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for the legal entity name" @@ -1827,6 +1876,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003010", "lbl" : "International Nonproprietary Name", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese." @@ -1853,6 +1903,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003011", "lbl" : "latin term", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing Latin term synonyms." @@ -1875,6 +1926,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003012", "lbl" : "acronym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms." @@ -1893,10 +1945,118 @@ "val" : "2023-11-01" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0004000", + "lbl" : "has symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A serial number such as \"12324X\"; a stop sign; a written proper name such as \"OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/144" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6523-4866" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2024-03-25" + } ] + } + }, { + "id" : "http://purl.org/dc/elements/1.1/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/coverage", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/format", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/identifier", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/language", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/publisher", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/relation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/rights", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/subject", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/created", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has broad synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." @@ -1912,10 +2072,34 @@ "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" } ] } + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", + "lbl" : "has cross-reference", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2024-03-18" + } ] + } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has exact synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." @@ -1935,6 +2119,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has narrow synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." @@ -1954,6 +2139,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has related synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." @@ -1974,10 +2160,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000027", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000030", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000078", "pred" : "is_a", diff --git a/omo-full.obo b/omo-full.obo index c9998d1..05d3b10 100644 --- a/omo-full.obo +++ b/omo-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: omo/releases/2023-11-02/omo-full.owl +data-version: omo/releases/2024-11-13/omo-full.owl synonymtypedef: OMO:0003000 "abbreviation" synonymtypedef: OMO:0003001 "ambiguous synonym" synonymtypedef: OMO:0003002 "dubious synonym" @@ -13,47 +13,51 @@ synonymtypedef: OMO:0003009 "legal name" synonymtypedef: OMO:0003010 "International Nonproprietary Name" synonymtypedef: OMO:0003011 "latin term" synonymtypedef: OMO:0003012 "acronym" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: protege http://protege.stanford.edu/plugins/owl/protege# +idspace: terms http://purl.org/dc/terms/ ontology: omo/omo-full -property_value: defaultLanguage "en" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Adam Goldstein" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Alan Ruttenberg" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Albert Goldfain" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Barry Smith" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Bjoern Peters" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Carlo Torniai" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Chris Stoeckert" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Christian A. Boelling" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Darren Natale" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Gwen Frishkoff" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Holger Stenzhorn" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "James A. Overton" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "James Malone" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Jennifer Fostel" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Jie Zheng" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Jonathan Rees" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Larisa Soldatova" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Lawrence Hunter" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Matt Brush" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Melanie Courtot" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Michel Dumontier" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Paolo Ciccarese" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Pat Hayes" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Philippe Rocca-Serra" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Randy Dipert" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Ron Rudnicki" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Satya Sahoo" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Sivaram Arabandi" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Werner Ceusters" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "William Duncan" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "William Hogan" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Yongqun (Oliver) He" xsd:string -property_value: http://purl.org/dc/elements/1.1/description "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)." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "OBO Metadata Ontology" xsd:string -property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ -property_value: owl:versionInfo "2023-11-02" xsd:string +property_value: dc:contributor "Adam Goldstein" xsd:string +property_value: dc:contributor "Alan Ruttenberg" xsd:string +property_value: dc:contributor "Albert Goldfain" xsd:string +property_value: dc:contributor "Barry Smith" xsd:string +property_value: dc:contributor "Bjoern Peters" xsd:string +property_value: dc:contributor "Carlo Torniai" xsd:string +property_value: dc:contributor "Chris Mungall" xsd:string +property_value: dc:contributor "Chris Stoeckert" xsd:string +property_value: dc:contributor "Christian A. Boelling" xsd:string +property_value: dc:contributor "Darren Natale" xsd:string +property_value: dc:contributor "David Osumi-Sutherland" xsd:string +property_value: dc:contributor "Gwen Frishkoff" xsd:string +property_value: dc:contributor "Holger Stenzhorn" xsd:string +property_value: dc:contributor "James A. Overton" xsd:string +property_value: dc:contributor "James Malone" xsd:string +property_value: dc:contributor "Jennifer Fostel" xsd:string +property_value: dc:contributor "Jie Zheng" xsd:string +property_value: dc:contributor "Jonathan Rees" xsd:string +property_value: dc:contributor "Larisa Soldatova" xsd:string +property_value: dc:contributor "Lawrence Hunter" xsd:string +property_value: dc:contributor "Mathias Brochhausen" xsd:string +property_value: dc:contributor "Matt Brush" xsd:string +property_value: dc:contributor "Melanie Courtot" xsd:string +property_value: dc:contributor "Michel Dumontier" xsd:string +property_value: dc:contributor "Paolo Ciccarese" xsd:string +property_value: dc:contributor "Pat Hayes" xsd:string +property_value: dc:contributor "Philippe Rocca-Serra" xsd:string +property_value: dc:contributor "Randy Dipert" xsd:string +property_value: dc:contributor "Ron Rudnicki" xsd:string +property_value: dc:contributor "Satya Sahoo" xsd:string +property_value: dc:contributor "Sivaram Arabandi" xsd:string +property_value: dc:contributor "Werner Ceusters" xsd:string +property_value: dc:contributor "William Duncan" xsd:string +property_value: dc:contributor "William Hogan" xsd:string +property_value: dc:contributor "Yongqun (Oliver) He" xsd:string +property_value: dc:description "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)." xsd:string +property_value: dc:title "OBO Metadata Ontology" xsd:string +property_value: owl:versionInfo "2024-11-13" xsd:string +property_value: protege:defaultLanguage "en" xsd:string +property_value: terms:license https://creativecommons.org/publicdomain/zero/1.0/ [Term] id: IAO:0000027 @@ -64,7 +68,6 @@ property_value: IAO:0000111 "data item" xsd:string [Term] id: IAO:0000030 name: information content entity -is_a: BFO:0000031 property_value: IAO:0000111 "information content entity" xsd:string [Term] diff --git a/omo-full.owl b/omo-full.owl index f16d748..210671d 100644 --- a/omo-full.owl +++ b/omo-full.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Adam Goldstein Alan Ruttenberg @@ -52,7 +52,7 @@ 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). OBO Metadata Ontology - 2023-11-02 + 2024-11-13 @@ -762,6 +762,19 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + A serial number such as "12324X"; a stop sign; a written proper name such as "OBI + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + + + 2024-03-25 + has symbol + + + + @@ -901,6 +914,19 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + + 2024-03-18 + has cross-reference + + + + @@ -968,12 +994,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - @@ -987,7 +1007,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - information content entity information content entity @@ -1635,5 +1654,5 @@ No imports - + diff --git a/omo.json b/omo.json index 64948c6..9933191 100644 --- a/omo.json +++ b/omo.json @@ -121,18 +121,28 @@ "val" : "https://creativecommons.org/publicdomain/zero/1.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-11-02" + "val" : "2024-11-13" } ], - "version" : "http://purl.obolibrary.org/obo/omo/releases/2023-11-02/omo.json" + "version" : "http://purl.obolibrary.org/obo/omo/releases/2024-11-13/omo.json" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_0000027", + "lbl" : "data item", + "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" + "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" } ] } }, { @@ -164,16 +174,16 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "lbl" : "failed exploratory term", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "lbl" : "data about an ontology part", + "type" : "CLASS", "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" + "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" : "failed exploratory term" + "val" : "data about an ontology part" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" @@ -205,532 +215,462 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_0000409", + "lbl" : "denotator type", + "type" : "CLASS", "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." + "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" : "metadata complete" + "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_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000000", + "lbl" : "ontology module", + "type" : "CLASS", "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" + "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_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000001", + "lbl" : "base ontology module", + "type" : "CLASS", "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.\"" + "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" : "ready for release" + "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_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000002", + "lbl" : "editors ontology module", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + "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" : "metadata incomplete" + "val" : "editors ontology module" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "source ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000003", + "lbl" : "main release ontology module", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + "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" : "uncurated" + "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_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000004", + "lbl" : "bridge ontology module", + "type" : "CLASS", "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." + "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" : "pending final vetting" + "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_0000226", - "lbl" : "placeholder removed", - "type" : "INDIVIDUAL", + "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" : "placeholder removed" + "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_0000227", - "lbl" : "terms merged", - "type" : "INDIVIDUAL", + "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" : "terms merged" + "val" : "subset ontology module" }, { - "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." + "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_0000228", - "lbl" : "term imported", - "type" : "INDIVIDUAL", + "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" : "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." + "val" : "curation subset ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "lbl" : "term split", - "type" : "INDIVIDUAL", + "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" : "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." + "val" : "analysis ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "lbl" : "universal", - "type" : "INDIVIDUAL", + "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" : "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" + "val" : "single layer ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribbon subset" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000409", - "lbl" : "denotator type", + "id" : "http://purl.obolibrary.org/obo/IAO_8000010", + "lbl" : "exclusion subset ontology module", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective." + "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" : "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" + "val" : "exclusion subset ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Barry Smith, Werner Ceusters" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "antislim" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "lbl" : "defined class", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000011", + "lbl" : "external import ontology module", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" + "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" : "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." + "val" : "external import ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "external import" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "lbl" : "named class expression", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000012", + "lbl" : "species subset ontology module", + "type" : "CLASS", "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." + "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" : "named class expression" + "val" : "species subset ontology module" }, { - "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_0000118", + "val" : "taxon subset" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" + "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_0000423", - "lbl" : "to be replaced with external ontology term", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000013", + "lbl" : "reasoned ontology module", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology." + "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" : "to be replaced with external ontology term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" + "val" : "reasoned ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/reason" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000014", + "lbl" : "generated ontology module", + "type" : "CLASS", "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." + "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" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" + "val" : "generated ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" + "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/OMO_0001000", - "lbl" : "out of scope", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000015", + "lbl" : "template generated ontology module", + "type" : "CLASS", "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." + "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_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_0000111", + "val" : "template generated ontology module" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/template" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://doi.org/10.1186/s13326-017-0126-0" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "https://orcid.org/0000-0001-5208-3432" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0001002", - "lbl" : "domain entity does not exist", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/IAO_8000016", + "lbl" : "taxonomic bridge ontology module", + "type" : "CLASS", "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" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "taxonomic bridge ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000027", - "lbl" : "data item", + "id" : "http://purl.obolibrary.org/obo/IAO_8000017", + "lbl" : "ontology module subsetted by expressivity", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data item" + "val" : "ontology module subsetted by expressivity" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000030", - "lbl" : "information content entity", + "id" : "http://purl.obolibrary.org/obo/IAO_8000018", + "lbl" : "obo basic subset ontology module", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "information content entity" + "val" : "obo basic subset ontology module" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000102", - "lbl" : "data about an ontology part", + "id" : "http://purl.obolibrary.org/obo/IAO_8000019", + "lbl" : "ontology module subsetted by OWL profile", "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" + "val" : "ontology module subsetted by OWL profile" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000111", - "lbl" : "editor preferred term", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_8000020", + "lbl" : "EL++ ontology module", + "type" : "CLASS", "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:" + "val" : "EL++ ontology module" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000112", - "lbl" : "example of usage", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL", "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:" + "val" : "example to be eventually removed" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000113", - "lbl" : "in branch", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet." + "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" : "in branch" + "val" : "failed exploratory term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "GROUP:OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000277" + "val" : "Person:Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000114", - "lbl" : "has curation status", - "type" : "PROPERTY", + "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" : "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" + "val" : "metadata complete" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", "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." + "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" : "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:" + "val" : "organizational term" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", "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." + "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" : "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:" + "val" : "ready for release" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000117", - "lbl" : "term editor", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", "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" + "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" : "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:" + "val" : "metadata incomplete" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000118", - "lbl" : "alternative label", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", "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." + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." }, - "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:" + "val" : "uncurated" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000119", - "lbl" : "definition source", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", "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" + "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" : "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:" + "val" : "pending final vetting" } ] } }, { @@ -754,833 +694,931 @@ "deprecated" : true } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "lbl" : "has obsolescence reason", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "type" : "INDIVIDUAL", "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" + "val" : "placeholder removed" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000232", - "lbl" : "curator note", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "type" : "INDIVIDUAL", "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" + "val" : "terms merged" }, { - "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" : "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_0000117", - "val" : "PERSON:Alan Ruttenberg" + "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_0000233", - "lbl" : "term tracker item", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "type" : "INDIVIDUAL", "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" + "val" : "term split" }, { - "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_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_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "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" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000234", - "lbl" : "ontology term requester", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition." + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, - "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" + "val" : "defined class" }, { - "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" : "\"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" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + "val" : "Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000411", - "lbl" : "is denotator type", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "Relates an class defined in an ontology, to the type of it's denotator" + "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" : "is denotator type" + "val" : "named class expression" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + "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_0000412", - "lbl" : "imported from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "For external terms/classes, the ontology from which the term was imported" + "val" : "Terms with this status should eventually replaced with a term from another ontology." }, "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" + "val" : "to be replaced with external ontology term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" + "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" + "val" : "group:OBI" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "lbl" : "expand expression to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", "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" + "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" : "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" + "val" : "requires discussion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000425", - "lbl" : "expand assertion to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom." + "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_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_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" : "Chris Mungall" + "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/IAO_0000426", - "lbl" : "first order logic expression", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/OMO_0001002", + "lbl" : "domain entity does not exist", + "type" : "INDIVIDUAL", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "first order logic expression" + "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" : "PERSON:Alan Ruttenberg" + "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_0000427", - "lbl" : "antisymmetric property", + "id" : "http://protege.stanford.edu/plugins/owl/protege#defaultLanguage", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "lbl" : "editor preferred term", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Use boolean value xsd:true to indicate that the property is an antisymmetric property" + "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" : "antisymmetric property" + "val" : "editor preferred term" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "part_of antisymmetric property xsd:true" + "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" : "Alan Ruttenberg" + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000589", - "lbl" : "OBO foundry unique label", + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl" : "example of usage", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An alternative name for a class or property which is unique across the OBO Foundry." + "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" : "OBO foundry unique label" + "val" : "example of usage" }, { "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" + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" + "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBO Foundry " + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000596", - "lbl" : "has ID digit count", + "id" : "http://purl.obolibrary.org/obo/IAO_0000113", + "lbl" : "in branch", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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)" + "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" : "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\"" + "val" : "in branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" + "val" : "GROUP:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000277" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000597", - "lbl" : "has ID range allocated to", + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "lbl" : "has curation status", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" + "val" : "has curation status" }, { - "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000598", - "lbl" : "has ID policy for", + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages" + "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" : "has ID policy for" + "val" : "definition" }, { - "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_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:Alan Ruttenberg" + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000599", - "lbl" : "has ID prefix", + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "has ID prefix" + "val" : "editor note" }, { - "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_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000600", - "lbl" : "elucidation", + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "lbl" : "term editor", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "elucidation" + "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:Alan Ruttenberg" + "val" : "PERSON:Daniel Schober" }, { "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" + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000601", - "lbl" : "has associated axiom(nl)", + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "lbl" : "alternative label", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "has associated axiom(nl)" + "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" : "Person:Alan Ruttenberg" + "val" : "OBO Operations committee" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An axiom associated with a term expressed using natural language" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000602", - "lbl" : "has associated axiom(fol)", + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "lbl" : "definition source", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "has associated axiom(fol)" + "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:Alan Ruttenberg" + "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An axiom expressed in first order logic using CLIF syntax" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000603", - "lbl" : "is allocated id range", + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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\"" + "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." }, - "comments" : [ "Add as annotation triples in the granting ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is allocated id range" + "val" : "has obsolescence reason" }, { "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" + "val" : "PERSON:Melanie Courtot" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0006011", - "lbl" : "may be identical to", + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "lbl" : "curator note", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "val" : "An administrative note of use for a curator but of no use for a user" }, - "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" + "val" : "curator note" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "#40" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "VFB" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0006012", - "lbl" : "scheduled for obsoletion on or after", + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date." + "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" : "scheduled for obsoletion on or after" + "val" : "term tracker item" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall, Jie Zheng" + "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_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/15532" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "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_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "GO ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0010000", - "lbl" : "has axiom label", + "id" : "http://purl.obolibrary.org/obo/IAO_0000234", + "lbl" : "ontology term requester", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "has axiom id" + "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:Alan Ruttenberg" + "val" : "Person: Jie Zheng, Chris Stoeckert, 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" + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", + "id" : "http://purl.obolibrary.org/obo/IAO_0000411", + "lbl" : "is denotator type", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" + "val" : "Relates an class defined in an ontology, to the type of it's denotator" }, - "comments" : [ "Add as annotation triples in the granting ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" + "val" : "is denotator type" }, { - "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" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" + "val" : "Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000000", - "lbl" : "ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000412", + "lbl" : "imported from", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "ontology module" + "val" : "imported from" }, { - "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_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ontology file" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" }, { - "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." + "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_8000001", - "lbl" : "base ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "base ontology module" + "val" : "expand expression to" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" + "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_8000002", - "lbl" : "editors ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000425", + "lbl" : "expand assertion to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "editors ontology module" + "val" : "expand assertion to" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "source ontology module" + "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_8000003", - "lbl" : "main release ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "lbl" : "first order logic expression", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" + "val" : "first order logic expression" }, { - "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" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000004", - "lbl" : "bridge ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000427", + "lbl" : "antisymmetric property", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "bridge ontology module" + "val" : "antisymmetric property" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + "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_8000005", - "lbl" : "import ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl" : "OBO foundry unique label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A subset ontology module that is intended to be imported from another ontology." + "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" : "import ontology module" + "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" : "TODO: add axioms that indicate this is the output of a module extraction process." + "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_0000118", - "val" : "import file" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://robot.obolibrary.org/extract" + "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_8000006", - "lbl" : "subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000596", + "lbl" : "has ID digit count", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." + "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" : "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" + "val" : "has ID digit count" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://robot.obolibrary.org/filter" + "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://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000007", - "lbl" : "curation subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000597", + "lbl" : "has ID range allocated to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "curation subset ontology module" + "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_8000008", - "lbl" : "analysis subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000598", + "lbl" : "has ID policy for", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An ontology module that is intended for usage in analysis or discovery applications." + "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" : "analysis ontology module" + "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_8000009", - "lbl" : "single layer subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000599", + "lbl" : "has ID prefix", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "single layer ontology module" + "val" : "has ID prefix" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ribbon subset" + "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_8000010", - "lbl" : "exclusion subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl" : "elucidation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" + "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_0000118", - "val" : "antislim" + "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_8000011", - "lbl" : "external import ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000601", + "lbl" : "has associated axiom(nl)", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" + "val" : "has associated axiom(nl)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "external import" + "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_8000012", - "lbl" : "species subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000602", + "lbl" : "has associated axiom(fol)", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" + "val" : "has associated axiom(fol)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "taxon subset" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://purl.obolibrary.org/obo/IAO_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_8000013", - "lbl" : "reasoned ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000603", + "lbl" : "is allocated id range", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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." + "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" : "reasoned ontology module" + "val" : "is allocated id range" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://robot.obolibrary.org/reason" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000014", - "lbl" : "generated ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "has ontology root term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." + "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" : "generated ontology module" + "val" : "has ontology root term" }, { - "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" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Nicolas Matentzoglu" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000015", - "lbl" : "template generated ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0006011", + "lbl" : "may be identical to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template." + "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" : "template generated ontology module" + "val" : "may be identical to" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://robot.obolibrary.org/template" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://doi.org/10.1186/s13326-017-0126-0" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "#40" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000016", - "lbl" : "taxonomic bridge ontology module", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "taxonomic bridge ontology module" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000017", - "lbl" : "ontology module subsetted by expressivity", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ontology module subsetted by expressivity" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "VFB" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_8000018", - "lbl" : "obo basic subset ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0006012", + "lbl" : "scheduled for obsoletion on or after", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" + "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" : "obo basic subset ontology module" + "val" : "scheduled for obsoletion on or after" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + "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_8000019", - "lbl" : "ontology module subsetted by OWL profile", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0010000", + "lbl" : "has axiom label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ontology module subsetted by OWL profile" + "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_8000020", - "lbl" : "EL++ ontology module", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "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" : "EL++ ontology module" + "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/OMO_0001001", "lbl" : "logical characteristic of object property", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL." @@ -1597,6 +1635,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0002000", "lbl" : "defined by construct", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." @@ -1619,6 +1658,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003000", "lbl" : "abbreviation", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing abbreviations or initalisms" @@ -1641,6 +1681,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003001", "lbl" : "ambiguous synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing ambiguous synonyms" @@ -1660,6 +1701,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003002", "lbl" : "dubious synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing dubious synonyms" @@ -1679,6 +1721,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003003", "lbl" : "layperson synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing layperson or colloquial synonyms" @@ -1701,6 +1744,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003004", "lbl" : "plural form", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing pluralization synonyms" @@ -1723,6 +1767,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003005", "lbl" : "UK spelling synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing UK spelling variants" @@ -1745,6 +1790,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003006", "lbl" : "misspelling", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for common misspellings" @@ -1764,6 +1810,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003007", "lbl" : "misnomer", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway" @@ -1783,6 +1830,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003008", "lbl" : "previous name", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for names that have been used as primary labels in the past." @@ -1805,6 +1853,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003009", "lbl" : "legal name", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for the legal entity name" @@ -1827,6 +1876,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003010", "lbl" : "International Nonproprietary Name", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese." @@ -1853,6 +1903,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003011", "lbl" : "latin term", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing Latin term synonyms." @@ -1875,6 +1926,7 @@ "id" : "http://purl.obolibrary.org/obo/OMO_0003012", "lbl" : "acronym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms." @@ -1893,10 +1945,118 @@ "val" : "2023-11-01" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0004000", + "lbl" : "has symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A serial number such as \"12324X\"; a stop sign; a written proper name such as \"OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/144" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6523-4866" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2024-03-25" + } ] + } + }, { + "id" : "http://purl.org/dc/elements/1.1/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/coverage", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/format", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/identifier", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/language", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/publisher", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/relation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/rights", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/subject", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/created", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has broad synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." @@ -1912,10 +2072,34 @@ "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" } ] } + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", + "lbl" : "has cross-reference", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2024-03-18" + } ] + } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has exact synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." @@ -1935,6 +2119,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has narrow synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." @@ -1954,6 +2139,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has related synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." @@ -1974,10 +2160,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000027", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000030", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000078", "pred" : "is_a", diff --git a/omo.obo b/omo.obo index 917576d..42f8b53 100644 --- a/omo.obo +++ b/omo.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2023-11-02 +data-version: releases/2024-11-13 synonymtypedef: OMO:0003000 "abbreviation" synonymtypedef: OMO:0003001 "ambiguous synonym" synonymtypedef: OMO:0003002 "dubious synonym" @@ -13,47 +13,51 @@ synonymtypedef: OMO:0003009 "legal name" synonymtypedef: OMO:0003010 "International Nonproprietary Name" synonymtypedef: OMO:0003011 "latin term" synonymtypedef: OMO:0003012 "acronym" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: protege http://protege.stanford.edu/plugins/owl/protege# +idspace: terms http://purl.org/dc/terms/ ontology: omo -property_value: defaultLanguage "en" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Adam Goldstein" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Alan Ruttenberg" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Albert Goldfain" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Barry Smith" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Bjoern Peters" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Carlo Torniai" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Chris Stoeckert" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Christian A. Boelling" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Darren Natale" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Gwen Frishkoff" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Holger Stenzhorn" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "James A. Overton" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "James Malone" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Jennifer Fostel" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Jie Zheng" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Jonathan Rees" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Larisa Soldatova" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Lawrence Hunter" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Matt Brush" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Melanie Courtot" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Michel Dumontier" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Paolo Ciccarese" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Pat Hayes" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Philippe Rocca-Serra" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Randy Dipert" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Ron Rudnicki" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Satya Sahoo" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Sivaram Arabandi" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Werner Ceusters" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "William Duncan" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "William Hogan" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "Yongqun (Oliver) He" xsd:string -property_value: http://purl.org/dc/elements/1.1/description "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)." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "OBO Metadata Ontology" xsd:string -property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ -property_value: owl:versionInfo "2023-11-02" xsd:string +property_value: dc:contributor "Adam Goldstein" xsd:string +property_value: dc:contributor "Alan Ruttenberg" xsd:string +property_value: dc:contributor "Albert Goldfain" xsd:string +property_value: dc:contributor "Barry Smith" xsd:string +property_value: dc:contributor "Bjoern Peters" xsd:string +property_value: dc:contributor "Carlo Torniai" xsd:string +property_value: dc:contributor "Chris Mungall" xsd:string +property_value: dc:contributor "Chris Stoeckert" xsd:string +property_value: dc:contributor "Christian A. Boelling" xsd:string +property_value: dc:contributor "Darren Natale" xsd:string +property_value: dc:contributor "David Osumi-Sutherland" xsd:string +property_value: dc:contributor "Gwen Frishkoff" xsd:string +property_value: dc:contributor "Holger Stenzhorn" xsd:string +property_value: dc:contributor "James A. Overton" xsd:string +property_value: dc:contributor "James Malone" xsd:string +property_value: dc:contributor "Jennifer Fostel" xsd:string +property_value: dc:contributor "Jie Zheng" xsd:string +property_value: dc:contributor "Jonathan Rees" xsd:string +property_value: dc:contributor "Larisa Soldatova" xsd:string +property_value: dc:contributor "Lawrence Hunter" xsd:string +property_value: dc:contributor "Mathias Brochhausen" xsd:string +property_value: dc:contributor "Matt Brush" xsd:string +property_value: dc:contributor "Melanie Courtot" xsd:string +property_value: dc:contributor "Michel Dumontier" xsd:string +property_value: dc:contributor "Paolo Ciccarese" xsd:string +property_value: dc:contributor "Pat Hayes" xsd:string +property_value: dc:contributor "Philippe Rocca-Serra" xsd:string +property_value: dc:contributor "Randy Dipert" xsd:string +property_value: dc:contributor "Ron Rudnicki" xsd:string +property_value: dc:contributor "Satya Sahoo" xsd:string +property_value: dc:contributor "Sivaram Arabandi" xsd:string +property_value: dc:contributor "Werner Ceusters" xsd:string +property_value: dc:contributor "William Duncan" xsd:string +property_value: dc:contributor "William Hogan" xsd:string +property_value: dc:contributor "Yongqun (Oliver) He" xsd:string +property_value: dc:description "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)." xsd:string +property_value: dc:title "OBO Metadata Ontology" xsd:string +property_value: owl:versionInfo "2024-11-13" xsd:string +property_value: protege:defaultLanguage "en" xsd:string +property_value: terms:license https://creativecommons.org/publicdomain/zero/1.0/ [Term] id: IAO:0000027 @@ -64,7 +68,6 @@ property_value: IAO:0000111 "data item" xsd:string [Term] id: IAO:0000030 name: information content entity -is_a: BFO:0000031 property_value: IAO:0000111 "information content entity" xsd:string [Term] diff --git a/omo.owl b/omo.owl index d3682cb..c8a1dc5 100644 --- a/omo.owl +++ b/omo.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Adam Goldstein Alan Ruttenberg @@ -52,7 +52,7 @@ 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). OBO Metadata Ontology - 2023-11-02 + 2024-11-13 @@ -762,6 +762,19 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + A serial number such as "12324X"; a stop sign; a written proper name such as "OBI + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + + + 2024-03-25 + has symbol + + + + @@ -901,6 +914,19 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + + 2024-03-18 + has cross-reference + + + + @@ -968,12 +994,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - @@ -987,7 +1007,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - information content entity information content entity @@ -1635,5 +1654,5 @@ No imports - + diff --git a/src/ontology/omo-edit.owl b/src/ontology/omo-edit.owl index f5cffed..bf9f8a9 100644 --- a/src/ontology/omo-edit.owl +++ b/src/ontology/omo-edit.owl @@ -760,6 +760,19 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + A serial number such as "12324X"; a stop sign; a written proper name such as "OBI + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + + + 2024-03-25 + has symbol + + + + @@ -899,6 +912,19 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + + 2024-03-18 + has cross-reference + + + + @@ -1626,5 +1652,5 @@ No imports - +