Package org.biopax.paxtools.model.level3

Interface ControlledVocabulary

All Superinterfaces:
BioPAXElement, Cloneable, Level3Element, 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.

  • Method Details

    • getTerm

      Set<String> getTerm()
      Returns:
      The external controlled vocabulary term.

    • addTerm

      void addTerm(String term)
      Parameters:
      term - The external controlled vocabulary term.

    • removeTerm

      void removeTerm(String term)
      Parameters:
      term - The external controlled vocabulary term.