Uses of Interface
ubic.basecode.ontology.model.OntologyTerm

Packages that use OntologyTerm

Package	Description
ubic.basecode.ontology.jena	Implementation of OntologyService using Apache Jena.
ubic.basecode.ontology.model
ubic.basecode.ontology.providers	This package contains baseCode built-in ontologies and a GenericOntologyService to implement your own ontologies.
ubic.basecode.ontology.simple	Simple ontology implementation.

Uses of OntologyTerm in ubic.basecode.ontology.jena

Methods in ubic.basecode.ontology.jena that return OntologyTerm

Modifier and Type	Method	Description
@Nullable OntologyTerm	AbstractOntologyService.findUsingAlternativeId(String alternativeId)
@Nullable OntologyTerm	AbstractOntologyService.getTerm(String uri)

Methods in ubic.basecode.ontology.jena that return types with arguments of type OntologyTerm

Modifier and Type	Method	Description
Collection<OntologySearchResult<OntologyTerm>>	AbstractOntologyService.findTerm(String search, int maxResults, boolean keepObsoletes)
Set<OntologyTerm>	AbstractOntologyService.getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
Set<OntologyTerm>	AbstractOntologyService.getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)

Method parameters in ubic.basecode.ontology.jena with type arguments of type OntologyTerm

Modifier and Type	Method	Description
Set<OntologyTerm>	AbstractOntologyService.getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
Set<OntologyTerm>	AbstractOntologyService.getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)

Uses of OntologyTerm in ubic.basecode.ontology.model

Subinterfaces of OntologyTerm in ubic.basecode.ontology.model

Modifier and Type	Interface	Description
interface	OntologyCardinalityRestriction
interface	OntologyClassRestriction
interface	OntologyDatatypeRestriction
interface	OntologyRestriction	Note: this only handle 'someof' and 'allof' restrictions, not cardinality.

Methods in ubic.basecode.ontology.model that return OntologyTerm

Modifier and Type	Method	Description
@Nullable OntologyTerm	OntologyIndividual.getInstanceOf()	Return the term that this is an instance of.
OntologyTerm	OntologyClassRestriction.getRestrictedTo()

Methods in ubic.basecode.ontology.model that return types with arguments of type OntologyTerm

Modifier and Type	Method	Description
default Collection<OntologyTerm>	OntologyTerm.getChildren(boolean direct)	Obtain the children of this term via subclasses and additional properties.
default Collection<OntologyTerm>	OntologyTerm.getChildren(boolean direct, boolean includeAdditionalProperties)
Collection<OntologyTerm>	OntologyTerm.getChildren(boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)	Obtain the children of this term via subclass relationships and possibly some additional properties.
default Collection<OntologyTerm>	OntologyTerm.getParents(boolean direct)	Note that any restriction superclasses are not returned, unless they are has_proper_part
default Collection<OntologyTerm>	OntologyTerm.getParents(boolean direct, boolean includeAdditionalProperties)
Collection<OntologyTerm>	OntologyTerm.getParents(boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
Collection<OntologyTerm>	ObjectProperty.getRange()

Uses of OntologyTerm in ubic.basecode.ontology.providers

Methods in ubic.basecode.ontology.providers that return OntologyTerm

Modifier and Type	Method	Description
OntologyTerm	AbstractDelegatingOntologyService.findUsingAlternativeId(String alternativeId)
@Nullable OntologyTerm	OntologyService.findUsingAlternativeId(String alternativeId)	Find a term using an alternative ID.
OntologyTerm	AbstractDelegatingOntologyService.getTerm(String uri)
@Nullable OntologyTerm	OntologyService.getTerm(String uri)	Looks for a OntologyTerm that has the match in URI given

Methods in ubic.basecode.ontology.providers that return types with arguments of type OntologyTerm

Modifier and Type	Method	Description
Collection<OntologySearchResult<OntologyTerm>>	AbstractDelegatingOntologyService.findTerm(String search, int maxResults, boolean keepObsoletes)
default Collection<OntologySearchResult<OntologyTerm>>	OntologyService.findTerm(String search, int maxResults)	Looks for any terms that match the given search string.
Collection<OntologySearchResult<OntologyTerm>>	OntologyService.findTerm(String search, int maxResults, boolean keepObsoletes)	Looks for any terms that match the given search string.
Set<OntologyTerm>	AbstractDelegatingOntologyService.getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
default Set<OntologyTerm>	OntologyService.getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties)	Obtain all the children of a given set of terms, excluding obsolete terms.
Set<OntologyTerm>	OntologyService.getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)	Obtain all the children of a given set of terms.
Set<OntologyTerm>	AbstractDelegatingOntologyService.getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
default Set<OntologyTerm>	OntologyService.getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties)	Obtain all the parents of a given set of terms, excluding obsolete terms.
Set<OntologyTerm>	OntologyService.getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)	Obtain all the parents of a given set of terms.

Method parameters in ubic.basecode.ontology.providers with type arguments of type OntologyTerm

Modifier and Type	Method	Description
Set<OntologyTerm>	AbstractDelegatingOntologyService.getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
default Set<OntologyTerm>	OntologyService.getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties)	Obtain all the children of a given set of terms, excluding obsolete terms.
Set<OntologyTerm>	OntologyService.getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)	Obtain all the children of a given set of terms.
Set<OntologyTerm>	AbstractDelegatingOntologyService.getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
default Set<OntologyTerm>	OntologyService.getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties)	Obtain all the parents of a given set of terms, excluding obsolete terms.
Set<OntologyTerm>	OntologyService.getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)	Obtain all the parents of a given set of terms.

Uses of OntologyTerm in ubic.basecode.ontology.simple

Classes in ubic.basecode.ontology.simple that implement OntologyTerm

Modifier and Type	Class	Description
class	OntologyTermSimple	A light-weight version of OntologyTerms.

Methods in ubic.basecode.ontology.simple that return types with arguments of type OntologyTerm

Modifier and Type	Method	Description
Collection<OntologyTerm>	OntologyTermSimple.getChildren(boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
Collection<OntologyTerm>	OntologyTermSimple.getParents(boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)