oboInOwl
type: Ontology
default-namespace: oboInOwl
has_obo_format_version: 1.2
comment: OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties

definition
type: AnnotationProperty

auto_generated_by
type: AnnotationProperty
database_cross_reference: oboFormat:auto_generated_by
has_obo_namespace: oboInOwl
id: oboInOwl:autoGeneratedBy
is metadata tag: true

consider
type: AnnotationProperty
definition: 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
database_cross_reference: oboFormat:consider
has_obo_namespace: oboInOwl
id: oboInOwl:consider
is metadata tag: true

Axiom
annotated source: consider
annotated property: definition
annotated target: 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
database_cross_reference: oboInOwl:cjm

has_alternative_id
type: AnnotationProperty
definition: An alternative identifier for this class; should follow ID syntax. These can result from class merges
database_cross_reference: oboFormat:alt_id
has_obo_namespace: oboInOwl
id: oboInOwl:hasAlternativeId
is metadata tag: true

Axiom
annotated source: has_alternative_id
annotated property: definition
annotated target: An alternative identifier for this class; should follow ID syntax. These can result from class merges
database_cross_reference: oboInOwl:cjm

has_broad_synonym
type: AnnotationProperty
definition: An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis
database_cross_reference: oboFormat:broad_synonym
has_obo_namespace: oboInOwl
id: oboInOwl:hasBroadSynonym
is metadata tag: true

Axiom
annotated source: has_broad_synonym
annotated property: definition
annotated target: An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis
database_cross_reference: oboInOwl:GOC

has_date
type: AnnotationProperty
database_cross_reference: oboFormat:date
has_obo_namespace: oboInOwl
id: oboInOwl:hasDate
is metadata tag: true

database_cross_reference
type: AnnotationProperty
database_cross_reference: oboFormat:xref
has_obo_namespace: oboInOwl
id: oboInOwl:hasDbXref
is metadata tag: true
label: has_dbxref

has_default_namespace
type: AnnotationProperty
database_cross_reference: oboFormat:default-namespace
has_obo_namespace: oboInOwl
id: oboInOwl:hasDefaultNamespace
is metadata tag: true

has_definition
type: AnnotationProperty
definition: a relation between a class and an instance of a oboInOwl:Definition
database_cross_reference: oboFormat:def
has_obo_namespace: oboInOwl
id: oboInOwl:hasDefinition
is metadata tag: true
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

Axiom
annotated source: has_definition
annotated property: definition
annotated target: a relation between a class and an instance of a oboInOwl:Definition
database_cross_reference: oboInOwl:cjm

has_exact_synonym
type: AnnotationProperty
definition: An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle
database_cross_reference: oboFormat:exact_synonym
has_obo_namespace: oboInOwl
id: oboInOwl:hasExactSynonym
is metadata tag: true

Axiom
annotated source: has_exact_synonym
annotated property: definition
annotated target: An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle
database_cross_reference: oboInOwl:GOC

has_narrow_synonym
type: AnnotationProperty
definition: 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
database_cross_reference: oboFormat:narrow_synonym
has_obo_namespace: oboInOwl
id: oboInOwl:hasNarrowSynonym
is metadata tag: true

Axiom
annotated source: has_narrow_synonym
annotated property: definition
annotated target: 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
database_cross_reference: oboInOwl:GOC

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty
definition: 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.
database_cross_reference: oboFormat:namespace
has_obo_namespace: oboInOwl
id: oboInOwl:hasOBONamespace
is metadata tag: true

Axiom
annotated source: has_obo_namespace
annotated property: definition
annotated target: 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.
database_cross_reference: oboInOwl:GOC

has_related_synonym
type: AnnotationProperty
definition: 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
database_cross_reference: oboFormat:related_synonym
has_obo_namespace: oboInOwl
id: oboInOwl:hasRelatedSynonym
is metadata tag: true

Axiom
annotated source: has_related_synonym
annotated property: definition
annotated target: 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
database_cross_reference: oboInOwl:GOC

has_subset
type: AnnotationProperty
definition: relation between an ontology and a oboInOwl:Subset, indicating classes in the ontology belong to the subset
has_obo_namespace: oboInOwl
id: oboInOwl:hasSubset
is metadata tag: true

Axiom
annotated source: has_subset
annotated property: definition
annotated target: relation between an ontology and a oboInOwl:Subset, indicating classes in the ontology belong to the subset
database_cross_reference: oboInOwl:cjm

has_synonym
type: AnnotationProperty
definition: A relation between a class and an alias term.
database_cross_reference: oboFormat:synonym
has_obo_namespace: oboInOwl
id: oboInOwl:hasSynonym
is metadata tag: true
comment: Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL

Axiom
annotated source: has_synonym
annotated property: definition
annotated target: A relation between a class and an alias term.
database_cross_reference: oboInOwl:GOC

has_synonym_type
type: AnnotationProperty
database_cross_reference: http://www.geneontology.org/GO.usage.shtml#type
has_obo_namespace: oboInOwl
id: oboInOwl:hasSynonymType
is metadata tag: true

has_URI
type: AnnotationProperty
has_obo_namespace: oboInOwl
id: oboInOwl:hasURI
is metadata tag: true

has_version
type: AnnotationProperty
database_cross_reference: oboFormat:version
has_obo_namespace: oboInOwl
id: oboInOwl:hasVersion
is metadata tag: true

id
type: AnnotationProperty
definition: relation between a class and its identifier as an OBO ID
has_obo_namespace: oboInOwl
id: oboInOwl:id
is metadata tag: true

Axiom
annotated source: id
annotated property: definition
annotated target: relation between a class and its identifier as an OBO ID
database_cross_reference: oboInOwl:jpb

in_subset
type: AnnotationProperty
definition: relation between a class and a oboInOwl:Subset, indicating the class belongs (is a member of) the subset
database_cross_reference: oboFormat:subset
has_obo_namespace: oboInOwl
id: oboInOwl:inSubset
is metadata tag: true

Axiom
annotated source: in_subset
annotated property: definition
annotated target: relation between a class and a oboInOwl:Subset, indicating the class belongs (is a member of) the subset
database_cross_reference: oboInOwl:cjm

is_cyclic
type: AnnotationProperty
definition: A relation R is cyclic if the following holds for some X, Y: X R Y, Y R X, X != Y
database_cross_reference: oboFormat:is_cyclic
has_obo_namespace: oboInOwl
id: oboInOwl:isCyclic
is metadata tag: true

Axiom
annotated source: is_cyclic
annotated property: definition
annotated target: A relation R is cyclic if the following holds for some X, Y: X R Y, Y R X, X != Y
database_cross_reference: oboInOwl:cjm

replaced_by
type: AnnotationProperty
definition: 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.
database_cross_reference: oboFormat:replaced_by
has_obo_namespace: oboInOwl
id: oboInOwl:replacedBy
is metadata tag: true

Axiom
annotated source: replaced_by
annotated property: definition
annotated target: 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.
database_cross_reference: oboInOwl:cjm

saved_by
type: AnnotationProperty
database_cross_reference: oboFormat:saved_by
has_obo_namespace: oboInOwl
id: oboInOwl:savedBy
is metadata tag: true

shorthand
type: AnnotationProperty
definition: relation between a relation and a human-readable term used to stand in for its identifier
has_obo_namespace: oboInOwl
id: oboInOwl:shorthand
is metadata tag: true

Axiom
annotated source: shorthand
annotated property: definition
annotated target: relation between a relation and a human-readable term used to stand in for its identifier
database_cross_reference: oboInOwl:jpb

obsolete_property
type: ObjectProperty
definition: pseudo-property. in the oboInOwl translation, all obsolete relations are subProperties of this class
has_obo_namespace: oboInOwl
id: oboInOwl:ObsoleteProperty
comment: Note that this is not a metaclass

Axiom
annotated source: obsolete_property
annotated property: definition
annotated target: pseudo-property. in the oboInOwl translation, all obsolete relations are subProperties of this class
database_cross_reference: oboInOwl:cjm

database_cross_reference
type: Class
database_cross_reference: http://www.w3.org/2000/01/rdf-schema#seeAlso
database_cross_reference: http://www.w3.org/2004/02/skos/core#related
has_obo_namespace: oboInOwl
id: oboInOwl:DbXref

definition
type: Class
definition: The textual definition of the current term. There must be zero or one instances of this tag per term description
database_cross_reference: http://www.obofoundry.org/wiki/index.php/Definitions
has_obo_namespace: oboInOwl
id: oboInOwl:Definition
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

Axiom
annotated source: definition
annotated property: definition
annotated target: The textual definition of the current term. There must be zero or one instances of this tag per term description
database_cross_reference: oboInOwl:cjm

obsolete_class
type: Class
definition: pseudo-class. in the oboInOwl translation, all obsolete classes are subclasses of this class. Note that this is not a metaclass
has_obo_namespace: oboInOwl
id: oboInOwl:ObsoleteClass

Axiom
annotated source: obsolete_class
annotated property: definition
annotated target: pseudo-class. in the oboInOwl translation, all obsolete classes are subclasses of this class. Note that this is not a metaclass
database_cross_reference: oboInOwl:cjm

subset
type: Class
definition: A grouping of terms from an ontology or ontologies. Note that this is not a metaclass - classes are linked to subsets via oboInOwl:inSubset
database_cross_reference: oboFormat:subsetdef
has_narrow_synonym: GO-slim
has_narrow_synonym: slim
has_obo_namespace: oboInOwl
has_related_synonym: partition
has_related_synonym: view
id: oboInOwl:Subset

Axiom
annotated source: subset
annotated property: definition
annotated target: A grouping of terms from an ontology or ontologies. Note that this is not a metaclass - classes are linked to subsets via oboInOwl:inSubset
database_cross_reference: oboInOwl:cjm

synonym
type: Class
definition: An instance of synonym usage. synonym instances are linked to classes via oboInOwl:has*Synonym properties
has_obo_namespace: oboInOwl
id: oboInOwl:Synonym
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

Axiom
annotated source: synonym
annotated property: definition
annotated target: An instance of synonym usage. synonym instances are linked to classes via oboInOwl:has*Synonym properties
database_cross_reference: oboInOwl:cjm

synonym_type
type: Class
has_obo_namespace: oboInOwl
id: oboInOwl:SynonymType