oboInOwl 1.2 OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties definition oboFormat:auto_generated_by oboInOwl oboInOwl:autoGeneratedBy true auto_generated_by Gives a term which may be an appropriate substitute for an obsolete term, but needs to be looked at carefully by a human expert before the replacement is done oboFormat:consider oboInOwl oboInOwl:consider true consider Gives a term which may be an appropriate substitute for an obsolete term, but needs to be looked at carefully by a human expert before the replacement is done oboInOwl:cjm An alternative identifier for this class; should follow ID syntax. These can result from class merges oboFormat:alt_id oboInOwl oboInOwl:hasAlternativeId true has_alternative_id An alternative identifier for this class; should follow ID syntax. These can result from class merges oboInOwl:cjm An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis oboFormat:broad_synonym oboInOwl oboInOwl:hasBroadSynonym true has_broad_synonym An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis oboInOwl:GOC oboFormat:date oboInOwl oboInOwl:hasDate true has_date oboFormat:xref oboInOwl oboInOwl:hasDbXref true database_cross_reference has_dbxref oboFormat:default-namespace oboInOwl oboInOwl:hasDefaultNamespace true has_default_namespace a relation between a class and an instance of a oboInOwl:Definition oboFormat:def oboInOwl oboInOwl:hasDefinition true we are forced to use the n-ary relation pattern in OWL1.0. For OWL2 we may make this a direct axiom between a class and the string has_definition a relation between a class and an instance of a oboInOwl:Definition oboInOwl:cjm An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle oboFormat:exact_synonym oboInOwl oboInOwl:hasExactSynonym true has_exact_synonym An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle oboInOwl:GOC An alias in which the alias is narrower than the primary class name. Example: pyrimidine-dimer repair by photolyase is a narrow synonym of photoreactive repair oboFormat:narrow_synonym oboInOwl oboInOwl:hasNarrowSynonym true has_narrow_synonym An alias in which the alias is narrower than the primary class name. Example: pyrimidine-dimer repair by photolyase is a narrow synonym of photoreactive repair oboInOwl:GOC has_obo_format_version A relation between a class and an OBO namespace string. OBO namespaces are to be distinguished from IDspaces; for example, biological_process is a namespace, GO is an idspace. oboFormat:namespace oboInOwl oboInOwl:hasOBONamespace true has_obo_namespace A relation between a class and an OBO namespace string. OBO namespaces are to be distinguished from IDspaces; for example, biological_process is a namespace, GO is an idspace. oboInOwl:GOC An alias in which the alias is related the primary class name, but not necessarily broader or narrower. Example: cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis oboFormat:related_synonym oboInOwl oboInOwl:hasRelatedSynonym true has_related_synonym An alias in which the alias is related the primary class name, but not necessarily broader or narrower. Example: cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis oboInOwl:GOC relation between an ontology and a oboInOwl:Subset, indicating classes in the ontology belong to the subset oboInOwl oboInOwl:hasSubset true has_subset relation between an ontology and a oboInOwl:Subset, indicating classes in the ontology belong to the subset oboInOwl:cjm A relation between a class and an alias term. oboFormat:synonym oboInOwl oboInOwl:hasSynonym true Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL has_synonym A relation between a class and an alias term. oboInOwl:GOC http://www.geneontology.org/GO.usage.shtml#type oboInOwl oboInOwl:hasSynonymType true has_synonym_type oboInOwl oboInOwl:hasURI true has_URI oboFormat:version oboInOwl oboInOwl:hasVersion true has_version relation between a class and its identifier as an OBO ID oboInOwl oboInOwl:id true id relation between a class and its identifier as an OBO ID oboInOwl:jpb relation between a class and a oboInOwl:Subset, indicating the class belongs (is a member of) the subset oboFormat:subset oboInOwl oboInOwl:inSubset true in_subset relation between a class and a oboInOwl:Subset, indicating the class belongs (is a member of) the subset oboInOwl:cjm A relation R is cyclic if the following holds for some X, Y: X R Y, Y R X, X != Y oboFormat:is_cyclic oboInOwl oboInOwl:isCyclic true is_cyclic A relation R is cyclic if the following holds for some X, Y: X R Y, Y R X, X != Y oboInOwl:cjm Gives a term which replaces an obsolete term. The value is the id of the replacement term. The value of this tag can safely be used to automatically reassign links to an obsolete term. The replaced_by tag may only be specified for obsolete terms. A single obsolete term may have more than one replaced_by tag. This tag can be used in conjunction with the consider tag. oboFormat:replaced_by oboInOwl oboInOwl:replacedBy true replaced_by Gives a term which replaces an obsolete term. The value is the id of the replacement term. The value of this tag can safely be used to automatically reassign links to an obsolete term. The replaced_by tag may only be specified for obsolete terms. A single obsolete term may have more than one replaced_by tag. This tag can be used in conjunction with the consider tag. oboInOwl:cjm oboFormat:saved_by oboInOwl oboInOwl:savedBy true saved_by relation between a relation and a human-readable term used to stand in for its identifier oboInOwl oboInOwl:shorthand true shorthand relation between a relation and a human-readable term used to stand in for its identifier oboInOwl:jpb pseudo-property. in the oboInOwl translation, all obsolete relations are subProperties of this class oboInOwl oboInOwl:ObsoleteProperty Note that this is not a metaclass obsolete_property pseudo-property. in the oboInOwl translation, all obsolete relations are subProperties of this class oboInOwl:cjm http://www.w3.org/2000/01/rdf-schema#seeAlso http://www.w3.org/2004/02/skos/core#related oboInOwl oboInOwl:DbXref database_cross_reference The textual definition of the current term. There must be zero or one instances of this tag per term description http://www.obofoundry.org/wiki/index.php/Definitions oboInOwl oboInOwl:Definition we are forced to use the n-ary relation pattern in OWL1.0. For OWL2 we may make this a direct axiom between a class and the string definition The textual definition of the current term. There must be zero or one instances of this tag per term description oboInOwl:cjm pseudo-class. in the oboInOwl translation, all obsolete classes are subclasses of this class. Note that this is not a metaclass oboInOwl oboInOwl:ObsoleteClass obsolete_class pseudo-class. in the oboInOwl translation, all obsolete classes are subclasses of this class. Note that this is not a metaclass oboInOwl:cjm A grouping of terms from an ontology or ontologies. Note that this is not a metaclass - classes are linked to subsets via oboInOwl:inSubset oboFormat:subsetdef GO-slim slim oboInOwl partition view oboInOwl:Subset subset A grouping of terms from an ontology or ontologies. Note that this is not a metaclass - classes are linked to subsets via oboInOwl:inSubset oboInOwl:cjm An instance of synonym usage. synonym instances are linked to classes via oboInOwl:has*Synonym properties oboInOwl oboInOwl:Synonym we are forced to use the n-ary relation pattern in OWL1.0. For OWL2 we may make this a direct axiom between a class and the string synonym An instance of synonym usage. synonym instances are linked to classes via oboInOwl:has*Synonym properties oboInOwl:cjm oboInOwl oboInOwl:SynonymType synonym_type