org.biojava.ontology
Interface Term

All Superinterfaces:

Annotatable, Changeable

All Known Subinterfaces:

OntologyTerm, RemoteTerm, Triple, Variable

All Known Implementing Classes:

AbstractTerm, IntegerOntology.IntTerm, OntologyTerm.Impl, RemoteTerm.Impl, Term.Impl, Triple.Impl, Variable.Impl

public interface Term

extends Annotatable

A term in an ontology. This has an Annotation which can be used for storing additional human-displayable information. It is strongly recommended that the Annotation is not used for any machine-readable data -- this should be represented by relations in the ontology instead.

Terms are things that represent things. They are the same sort of thing as a Java object or a prolog atom. A sub-set of terms are themselves relations. This means that they are used to describe associations between pairs of terms. Since all terms can be described, it is possible (and indeed encouraged) to describe relations. As a minimum, you should consider saying if they are identity or partial order relations, or if they are transitive, reflexive, symmetrical, anti-symmetrical or anything else you know about them. This gives the inference engine some chance of working out what is going on.

Since:

1.4

Author:

Thomas Down, Matthew Pocock

Nested Class Summary

static class

Term.Impl Simple in-memory implementation of an ontology term.

Nested classes inherited from class org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

static ChangeType

ONTOLOGY ChangeType which indicates that this term's ontology has been altered

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

String	getDescription() Return a human-readable description of this term, or the empty string if none is available.
String	getName() Return the name of this term.
Ontology	getOntology() Return the ontology in which this term exists.

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

ONTOLOGY

public static final ChangeType ONTOLOGY

ChangeType which indicates that this term's ontology has been altered

Method Detail

getName

public String getName()

Return the name of this term.

getDescription

public String getDescription()

Return a human-readable description of this term, or the empty string if none is available.

getOntology

public Ontology getOntology()

Return the ontology in which this term exists.