Package org.biojava.ontology

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.

Some interfaces and implementations from this package are extended in biojavax to better facilitate their persistence to biosql.

Interface Summary

Interface	Description
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

Class	Description
AbstractTerm	Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
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.
Synonym
Term.Impl	Simple in-memory implementation of an ontology term.
Triple.Impl	Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple
Variable.Impl

Exception Summary

Exception	Description
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