OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi database_cross_reference 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 The textual definition of the current term. There must be zero or one instances of this tag per term description oboInOwl:cjm http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm URL:http://www.obofoundry.org/wiki/index.php/Definitions http://www.obofoundry.org/wiki/index.php/Definitions 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 http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm 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 http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm view partition slim GO-slim oboFormat:subsetdef http://purl.org/obo/owl/oboFormat#oboFormat_subsetdef 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 An instance of synonym usage. synonym instances are linked to classes via oboInOwl:has*Synonym properties oboInOwl:cjm http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm synonym_type obsolete_property Note that this is not a metaclass pseudo-property. in the oboInOwl translation, all obsolete relations are subProperties of this class oboInOwl:cjm http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm 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 http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm oboFormat:consider http://purl.org/obo/owl/oboFormat#oboFormat_consider has_alternative_id An alternative identifier for this class; should follow ID syntax. These can result from class merges oboInOwl:cjm http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm oboFormat:alt_id http://purl.org/obo/owl/oboFormat#oboFormat_alt_id 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 http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC oboFormat:broad_synonym http://purl.org/obo/owl/oboFormat#oboFormat_broad_synonym has_date oboFormat:date http://purl.org/obo/owl/oboFormat#oboFormat_date has_dbxref oboFormat:xref http://purl.org/obo/owl/oboFormat#oboFormat_xref has_default_namespace oboFormat:default-namespace http://purl.org/obo/owl/oboFormat#oboFormat_default-namespace has_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 a relation between a class and an instance of a oboInOwl:Definition oboInOwl:cjm http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm oboFormat:def http://purl.org/obo/owl/oboFormat#oboFormat_def has_exact_synonym An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle oboInOwl:GOC http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC oboFormat:exact_synonym http://purl.org/obo/owl/oboFormat#oboFormat_exact_synonym 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 http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC oboFormat:narrow_synonym http://purl.org/obo/owl/oboFormat#oboFormat_narrow_synonym 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 http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC oboFormat:namespace http://purl.org/obo/owl/oboFormat#oboFormat_namespace has_synonym Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL A relation between a class and an alias term. oboInOwl:GOC http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC oboFormat:synonym http://purl.org/obo/owl/oboFormat#oboFormat_synonym 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 http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC oboFormat:related_synonym http://purl.org/obo/owl/oboFormat#oboFormat_related_synonym has_subset relation between an ontology and a oboInOwl:Subset, indicating classes in the ontology belong to the subset oboInOwl:cjm http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm has_synonym_type URL:http://www.geneontology.org/GO.usage.shtml#type http://www.geneontology.org/GO.usage.shtml#type has_URI has_version oboFormat:version http://purl.org/obo/owl/oboFormat#oboFormat_version in_subset relation between a class and a oboInOwl:Subset, indicating the class belongs (is a member of) the subset oboInOwl:cjm http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm oboFormat:subset http://purl.org/obo/owl/oboFormat#oboFormat_subset 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 http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm oboFormat:replaced_by http://purl.org/obo/owl/oboFormat#oboFormat_replaced_by saved_by oboFormat:saved_by http://purl.org/obo/owl/oboFormat#oboFormat_saved_by is_cyclic oboFormat:is_cyclic http://purl.org/obo/owl/oboFormat#oboFormat_is_cyclic subset_property This annotation property groups all subsets declared in the ontology oboInOwl:GOC http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC synonym_type_property This annotation property groups all synonym types declared in the ontology oboInOwl:GOC http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC