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
Interface Summary Interface Description OntologyAn ontology. OntologyFactoryA factory for Ontology instances. OntologyOpsThis is an interface for optimizing ontology operators. OntologyTermA term in an ontology which identifies another ontology. RemoteTermA term in another ontology. TermA term in an ontology. TripleA triple in an ontology. Variable
Class Summary Class Description AbstractTermAbstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties. DefaultOpsDefault implementation of OntologyOps. IntegerOntology Ontology.ImplA basic in-memory implementation of an ontology OntologyTerm.ImplSimple in-memory implementation of a remote ontology term. OntoToolsTools for manipulating ontologies. RemoteTerm.ImplSimple in-memory implementation of a remote ontology term. Synonym Term.ImplSimple in-memory implementation of an ontology term. Triple.ImplBasic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple Variable.Impl
Exception Summary Exception Description AlreadyExistsExceptionThrown to indicate that a term or triple can't be added to an ontology because it is already present. InvalidTermExceptionThrown to indicate that an ontology term is not acceptable or appropriate in a given context OntologyExceptionThrown to indicate an error in an Ontology object