Package ubic.basecode.ontology.model

Interface OntologyTerm

All Superinterfaces:

OntologyResource

All Known Subinterfaces:

OntologyCardinalityRestriction, OntologyClassRestriction, OntologyDatatypeRestriction, OntologyRestriction

All Known Implementing Classes:

OntologyTermSimple

public interface OntologyTerm
extends OntologyResource

Author:

Paul

Method Summary

Modifier and Type	Method	Description
Collection<String>	getAlternativeIds()	Obtain alternative IDs for this term.
@Nullable AnnotationProperty	getAnnotation(String propertyUri)	Obtain an annotation by property URI.
Collection<AnnotationProperty>	getAnnotations()	Obtain all annotations for this term.
Collection<AnnotationProperty>	getAnnotations(String propertyUri)	Obtain all the annotations for a given property URI.
default Collection<OntologyTerm>	getChildren(boolean direct)	Obtain the children of this term via subclasses and additional properties.
default Collection<OntologyTerm>	getChildren(boolean direct, boolean includeAdditionalProperties)
Collection<OntologyTerm>	getChildren(boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)	Obtain the children of this term via subclass relationships and possibly some additional properties.
default Collection<OntologyIndividual>	getIndividuals()
Collection<OntologyIndividual>	getIndividuals(boolean direct)
default Collection<OntologyTerm>	getParents(boolean direct)	Note that any restriction superclasses are not returned, unless they are has_proper_part
default Collection<OntologyTerm>	getParents(boolean direct, boolean includeAdditionalProperties)
Collection<OntologyTerm>	getParents(boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
Collection<OntologyRestriction>	getRestrictions()
@Nullable String	getTerm()	Deprecated. use OntologyResource.getLabel() instead.
boolean	isRoot()
boolean	isTermObsolete()	Deprecated. use OntologyResource.isObsolete() instead

Methods inherited from interface ubic.basecode.ontology.model.OntologyResource

getComment, getLabel, getLocalName, getUri, isObsolete, unwrap

Method Details

getAlternativeIds

Collection<String> getAlternativeIds()

Obtain alternative IDs for this term.

getAnnotations

Collection<AnnotationProperty> getAnnotations()

Obtain all annotations for this term.

getAnnotations

Collection<AnnotationProperty> getAnnotations(String propertyUri)

Obtain all the annotations for a given property URI.

getAnnotation

@Nullable AnnotationProperty getAnnotation(String propertyUri)

Obtain an annotation by property URI.

getChildren

default Collection<OntologyTerm> getChildren(boolean direct)

Obtain the children of this term via subclasses and additional properties.

See Also:

• getChildren(boolean, boolean)

getChildren

default Collection<OntologyTerm> getChildren(boolean direct,
 boolean includeAdditionalProperties)

getChildren

Collection<OntologyTerm> getChildren(boolean direct,
 boolean includeAdditionalProperties,
 boolean keepObsoletes)

Obtain the children of this term via subclass relationships and possibly some additional properties.

Parameters:

direct - return only the immediate children; if false, return all of them down to the leaves.

includeAdditionalProperties - include terms matched via additional properties

getIndividuals

default Collection<OntologyIndividual> getIndividuals()

getIndividuals

Collection<OntologyIndividual> getIndividuals(boolean direct)

getParents

default Collection<OntologyTerm> getParents(boolean direct)

Note that any restriction superclasses are not returned, unless they are has_proper_part

Parameters:

direct -

Returns:

getParents

default Collection<OntologyTerm> getParents(boolean direct,
 boolean includeAdditionalProperties)

getParents

Collection<OntologyTerm> getParents(boolean direct,
 boolean includeAdditionalProperties,
 boolean keepObsoletes)

getRestrictions

Collection<OntologyRestriction> getRestrictions()

getTerm

@Deprecated
@Nullable String getTerm()

Deprecated.

use OntologyResource.getLabel() instead.

isRoot

boolean isRoot()

isTermObsolete

@Deprecated
boolean isTermObsolete()

Deprecated.

use OntologyResource.isObsolete() instead

check to see if the term is obsolete, if it is it should not be used