org.biopax.paxtools.model.level3
Interface ControlledVocabulary

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Level3Element, java.io.Serializable, UtilityClass, XReferrable

All Known Subinterfaces:

CellularLocationVocabulary, CellVocabulary, EntityReferenceTypeVocabulary, EvidenceCodeVocabulary, ExperimentalFormVocabulary, InteractionVocabulary, PhenotypeVocabulary, RelationshipTypeVocabulary, SequenceModificationVocabulary, SequenceRegionVocabulary, TissueVocabulary

All Known Implementing Classes:

CellularLocationVocabularyImpl, CellVocabularyImpl, ControlledVocabularyImpl, EntityReferenceTypeVocabularyImpl, EvidenceCodeVocabularyImpl, ExperimentalFormVocabularyImpl, InteractionVocabularyImpl, PhenotypeVocabularyImpl, RelationshipTypeVocabularyImpl, SequenceModificationVocabularyImpl, SequenceRegionVocabularyImpl, TissueVocabularyImpl

public interface ControlledVocabulary
extends UtilityClass, XReferrable

Definition: This class represents a term from an external controlled vocabulary (CV).

Rationale: Controlled Vocabularies mark cases where BioPAX delegates the representation of a complex biological phenomena to an external controlled vocabulary development effort such as Gene Ontology. Each subclass of this class represents one such case and often has an associated "Best-Practice" external resource to use. See the documentation of each subclass for more specific information. Correct usage of controlled vocabularies are critical to data exchange and integration.

Usage: The individuals belonging to this class must unambiguously refer to the source controlled vocabulary. This can be achieved in two manners:

The xref property of this class is restricted to the unification xref class. It must point to the source controlled vocabulary.

Alternatively the rdf-id of the member individuals can be set to the designated MIRIAM URN.

It is a best practice to do both whenever possible.

Although it is possible to use multiple unification xrefs to identify semantically identical terms across alternative controlled vocabularies, this is not a recommended practice as it might lead to maintenance issues as the controlled vocabularies change.

There is no recommended use-cases for directly instantiating this class. Please, use its subclasses instead.

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

void	addTerm(java.lang.String term)
java.util.Set<java.lang.String>	getTerm()
void	removeTerm(java.lang.String term)

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Method Detail

getTerm

java.util.Set<java.lang.String> getTerm()

Returns:

The external controlled vocabulary term.

addTerm

void addTerm(java.lang.String term)

Parameters:

term - The external controlled vocabulary term.

removeTerm

void removeTerm(java.lang.String term)

Parameters:

term - The external controlled vocabulary term.