- 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.