org.biojava.ontology

Interface Term

All Superinterfaces:

Annotatable, Changeable

All Known Subinterfaces:

ComparableTerm, ComparableTriple, OntologyTerm, RemoteTerm, Triple, Variable

All Known Implementing Classes:

AbstractTerm, IntegerOntology.IntTerm, OntologyTerm.Impl, RemoteTerm.Impl, SimpleComparableTerm, SimpleComparableTriple, 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

See Also:

ComparableTerm

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	Term.Impl Simple in-memory implementation of an ontology term.

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field and Description
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

Methods

Modifier and Type	Method and Description
void	addSynonym(Object synonym) Add a synonym for this term.
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.
Object[]	getSynonyms() Return the synonyms for this term.
void	removeSynonym(Object synonym) Remove a synonym for this term.
void	setDescription(String description) set the description of the term;

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

static final ChangeType ONTOLOGY

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

Method Detail

getName

String getName()

Return the name of this term.

Returns:

the name of the term

getDescription

String getDescription()

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

Returns:

the description of the term

setDescription

void setDescription(String description)

set the description of the term;

Parameters:

description -

getOntology

Ontology getOntology()

Return the ontology in which this term exists.

Returns:

the ontology

getSynonyms

Object[] getSynonyms()

Return the synonyms for this term.

Returns:

the synonyms

addSynonym

void addSynonym(Object synonym)

Add a synonym for this term.

Parameters:

synonym - the synonym

removeSynonym

void removeSynonym(Object synonym)

Remove a synonym for this term.

Parameters:

synonym -