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.

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