public interface ControlledVocabulary extends UtilityClass, XReferrable
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.
UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT| Modifier and Type | Method and Description |
|---|---|
void |
addTerm(String term) |
Set<String> |
getTerm() |
void |
removeTerm(String term) |
addXref, getXref, removeXrefaddComment, getComment, removeCommentequivalenceCode, getAnnotations, getModelInterface, getUri, isEquivalentCopyright © 2017 BioPAX. All rights reserved.