Package org.biojava.ontology

A general-purpose API for ontologies.

See:
Description

Interface Summary

Ontology	An ontology.
OntologyFactory	A factory for Ontology instances.
OntologyOps	This is an interface for optimizing ontology operators.
OntologyTerm	A term in an ontology which identifies another ontology.
RemoteTerm	A term in another ontology.
Term	A term in an ontology.
Triple	A triple in an ontology.
Variable

Class Summary

AbstractTerm	Abstract implementation of term
DefaultOps	Default implementation of OntologyOps.
IntegerOntology
Ontology.Impl	A basic in-memory implementation of an ontology
OntologyTerm.Impl	Simple in-memory implementation of a remote ontology term.
OntoTools	Tools for manipulating ontologies.
RemoteTerm.Impl	Simple in-memory implementation of a remote ontology term.
Term.Impl	Simple in-memory implementation of an ontology term.
Triple.Impl	Basic in-memory implementation of a Triple in an ontology
Variable.Impl

Exception Summary

AlreadyExistsException	Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
InvalidTermException	Thrown to indicate that an ontology term is not acceptable or appropriate in a given context
OntologyException	Thrown to indicate an error in an Ontology object

Package org.biojava.ontology Description

A general-purpose API for ontologies. These are directed graphs consisting of Term obects. Each edge in the graph is annotated with a term which defines the relationship between its subject and object terms. In this API, these annotated edges are called triples.