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## 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.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
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 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
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
Ontology An ontology.
Synonym

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

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