Package org.biojava.nbio.ontology

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.
App	Hello world!
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