Package ubic.basecode.ontology.model

Interface OntologyTerm

All Superinterfaces:

Comparable<OntologyResource>, 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.
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()
String	getTerm()	Deprecated. use OntologyResource.getLabel() instead.
boolean	isRoot()
boolean	isTermObsolete()	Deprecated. use OntologyResource.isObsolete() instead

Methods inherited from interface java.lang.Comparable

compareTo

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

getComment, getLabel, getLocalName, getScore, getUri, isObsolete

Method Detail

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
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