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[Don't merge] Update oboInOwl.obo #26371

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[Don't merge] Update oboInOwl.obo #26371

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179 changes: 16 additions & 163 deletions contrib/oboInOwl.obo
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format-version: 1.2
remark: \n 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\n
remark: OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# ""
idspace: rdfs http://www.w3.org/2000/01/rdf-schema# ""
idspace: skos http://www.w3.org/2004/02/skos/core# ""
idspace: _base http://www.geneontology.org/formats/oboInOwl# ""
default-namespace: oboInOwl
ontology: http://www.geneontology.org/formats/oboInOwl
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym>))\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym>))\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym>))\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasSynonym>))\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> (<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym>)\n\nSubAnnotationPropertyOf(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://www.geneontology.org/formats/oboInOwl#hasSynonym>)\n\n# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> (<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>)\n\nSubAnnotationPropertyOf(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://www.geneontology.org/formats/oboInOwl#hasSynonym>)\n\n# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> (<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym>)\n\nSubAnnotationPropertyOf(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://www.geneontology.org/formats/oboInOwl#hasSynonym>)\n\n# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> (<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym>)\n\nSubAnnotationPropertyOf(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://www.geneontology.org/formats/oboInOwl#hasSynonym>)\n\n\n)

[Term]
id: oboInOwl:DbXref
id: DbXref
name: database_cross_reference
xref: http://www.w3.org/2000/01/rdf-schema#seeAlso
xref: http://www.w3.org/2004/02/skos/core#related

[Term]
id: oboInOwl:Definition
id: Definition
name: definition
def: "The textual definition of the current term. There must be zero or one instances of this tag per term description" [oboInOwl:cjm]
xref: http://www.obofoundry.org/wiki/index.php/Definitions
comment: 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
xref: _:genid2147483653

[Term]
id: oboInOwl:ObsoleteClass
id: ObsoleteClass
name: obsolete_class
def: "pseudo-class. in the oboInOwl translation, all obsolete classes are subclasses of this class. Note that this is not a metaclass" [oboInOwl:cjm]

[Term]
id: oboInOwl:Subset
xref: oboFormat:subsetdef
id: Subset
name: subset
synonym: "view" RELATED []
synonym: "partition" RELATED []
synonym: "slim" NARROW []
synonym: "GO-slim" NARROW []
def: "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]
synonym: "_:genid2147483663" RELATED []
synonym: "_:genid2147483665" RELATED []
synonym: "_:genid2147483667" NARROW []
synonym: "_:genid2147483669" NARROW []
xref: _:genid2147483671

[Term]
id: oboInOwl:Synonym
id: Synonym
name: synonym
def: "An instance of synonym usage. synonym instances are linked to classes via oboInOwl:has*Synonym properties" [oboInOwl:cjm]
comment: 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

[Term]
id: oboInOwl:SynonymType
id: SynonymType
name: synonym_type

[Typedef]
id: oboInOwl:ObsoleteProperty
id: ObsoleteProperty
name: obsolete_property
def: "pseudo-property. in the oboInOwl translation, all obsolete relations are subProperties of this class" [oboInOwl:cjm]
comment: Note that this is not a metaclass

[Typedef]
id: oboInOwl:autoGeneratedBy
xref: oboFormat:auto_generated_by
name: auto_generated_by
is_metadata_tag: true

[Typedef]
id: oboInOwl:consider
name: consider
xref: oboFormat:consider
def: "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]
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasAlternativeId
name: has_alternative_id
xref: oboFormat:alt_id
def: "An alternative identifier for this class; should follow ID syntax. These can result from class merges" [oboInOwl:cjm]
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasBroadSynonym
xref: oboFormat:broad_synonym
name: has_broad_synonym
def: "An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis" [oboInOwl:GOC]
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasDate
xref: oboFormat:date
name: has_date
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasDbXref
xref: oboFormat:xref
name: has_dbxref
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasDefaultNamespace
xref: oboFormat:default-namespace
name: has_default_namespace
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasDefinition
xref: oboFormat:def
name: has_definition
def: "a relation between a class and an instance of a oboInOwl:Definition" [oboInOwl:cjm]
comment: 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
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasExactSynonym
xref: oboFormat:exact_synonym
name: has_exact_synonym
def: "An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle" [oboInOwl:GOC]
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasNarrowSynonym
xref: oboFormat:narrow_synonym
name: has_narrow_synonym
def: "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]
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasOBONamespace
xref: oboFormat:namespace
def: "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]
name: has_obo_namespace
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasSynonym
xref: oboFormat:synonym
name: has_synonym
def: "A relation between a class and an alias term." [oboInOwl:GOC]
comment: Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasRelatedSynonym
xref: oboFormat:related_synonym
name: has_related_synonym
def: "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]
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasSubset
name: has_subset
def: "relation between an ontology and a oboInOwl:Subset, indicating classes in the ontology belong to the subset" [oboInOwl:cjm]
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasSynonymType
name: has_synonym_type
is_metadata_tag: true
xref: http://www.geneontology.org/GO.usage.shtml#type

[Typedef]
id: oboInOwl:hasURI
name: has_URI
is_metadata_tag: true

[Typedef]
id: oboInOwl:hasVersion
xref: oboFormat:version
name: has_version
is_metadata_tag: true

[Typedef]
id: oboInOwl:inSubset
name: in_subset
xref: oboFormat:subset
def: "relation between a class and a oboInOwl:Subset, indicating the class belongs (is a member of) the subset" [oboInOwl:cjm]
is_metadata_tag: true

[Typedef]
id: oboInOwl:replacedBy
xref: oboFormat:replaced_by
name: replaced_by
def: "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]
is_metadata_tag: true

[Typedef]
id: oboInOwl:savedBy
xref: oboFormat:saved_by
name: saved_by
is_metadata_tag: true

[Typedef]
id: oboInOwl:isCyclic
xref: oboFormat:is_cyclic
name: is_cyclic
def: "A relation R is cyclic if the following holds for some X, Y: X R Y, Y R X, X != Y" [oboInOwl:cjm]
is_metadata_tag: true
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