## Uses of Package
org.biojava.ontology

Packages that use org.biojava.ontology
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.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
Ontology An ontology.
Term A term in an ontology.

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

Classes in org.biojava.ontology used by org.biojava.bio.seq.impl
Term A term in an ontology.

Classes in org.biojava.ontology used by org.biojava.ontology
AbstractTerm Abstract implementation of term
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.
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
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.biojavax.bio.seq
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
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