Uses of Package
org.biojava.ontology

Packages that use org.biojava.ontology

Package	Description
org.biojava.bio.program.gff3	Support for reading and writing GFF3.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.ontology	A general-purpose API for ontologies.
org.biojava.ontology.io	Tools for loading and saving ontologies.
org.biojava.ontology.obo
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.

Classes in org.biojava.ontology used by org.biojava.bio.program.gff3

Class and Description
Ontology An ontology.
Term A term in an ontology.

Classes in org.biojava.ontology used by org.biojava.bio.seq

Class and Description
InvalidTermException Thrown to indicate that an ontology term is not acceptable or appropriate in a given context
Term A term in an ontology.

Classes in org.biojava.ontology used by org.biojava.bio.seq.db.biosql

Class and Description
Ontology An ontology.

Classes in org.biojava.ontology used by org.biojava.bio.seq.impl

Class and Description
Term A term in an ontology.

Classes in org.biojava.ontology used by org.biojava.ontology

Class and Description
AbstractTerm Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
AlreadyExistsException Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
IntegerOntology
IntegerOntology.IntTerm
Ontology An ontology.
OntologyException Thrown to indicate an error in an Ontology object
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.
Synonym
Term A term in an ontology.
Term.Impl Simple in-memory implementation of an ontology term.
Triple A triple in an ontology.
Variable

Classes in org.biojava.ontology used by org.biojava.ontology.io

Class and Description
Ontology An ontology.
OntologyException Thrown to indicate an error in an Ontology object
OntologyFactory A factory for Ontology instances.

Classes in org.biojava.ontology used by org.biojava.ontology.obo

Class and Description
Ontology An ontology.
Synonym

Classes in org.biojava.ontology used by org.biojavax.bio.seq

Class and Description
InvalidTermException Thrown to indicate that an ontology term is not acceptable or appropriate in a given context
Term A term in an ontology.

Classes in org.biojava.ontology used by org.biojavax.ontology

Class and Description
AlreadyExistsException Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
Ontology An ontology.
OntologyOps This is an interface for optimizing ontology operators.
Term A term in an ontology.
Triple A triple in an ontology.
Variable