## Uses of Interface
org.biojava.ontology.Ontology

Packages that use Ontology
org.biojava.bio.program.gff3: Support for reading and writing GFF3.
org.biojava.bio.seq.db.biosql: General purpose Sequence storage in a relational database.
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.ontology: Extensions to the biojava ontology model that represent BioSQL ontology.

Uses of Ontology in org.biojava.bio.program.gff3

Methods in org.biojava.bio.program.gff3 with parameters of type Ontology
`protected GFF3Record` `GFF3Parser.createRecord(GFF3DocumentHandler handler, List aList, String rest, String comment, Ontology ontology, Ontology fallBack)` Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.
`void` `GFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology)` Informs handler of each line of gff read from bReader.
`void` `GFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology, String locator)` Informs handler of each line of GFF read from bReader
`protected void` `GFF3Parser.parseAttribute(String attValList, Annotation anno, Ontology onto, Ontology fallBack)` Parse attValList into a Map of attributes and value lists.

Uses of Ontology in org.biojava.bio.seq.db.biosql

Methods in org.biojava.bio.seq.db.biosql that return Ontology
`Ontology` `BioSQLSequenceDB.addOntology(Ontology onto)` Deprecated.
`Ontology` `BioSQLSequenceDB.createOntology(String name, String description)` Deprecated.
`Ontology` `BioSQLSequenceDB.getOntology(String name)` Deprecated.

Methods in org.biojava.bio.seq.db.biosql with parameters of type Ontology
`Ontology` `BioSQLSequenceDB.addOntology(Ontology onto)` Deprecated.

Uses of Ontology in org.biojava.ontology

Classes in org.biojava.ontology that implement Ontology
`class` `IntegerOntology`
`static class` `Ontology.Impl` A basic in-memory implementation of an ontology

Methods in org.biojava.ontology that return Ontology
`Ontology` `OntologyFactory.createOntology(String name, String description)` Creates a new Ontology
`static Ontology` `OntoTools.getCoreOntology()` Get the Ontology that defines our core "central dogma".
`Ontology` `Triple.Impl.getOntology()`
`Ontology` `Term.getOntology()` Return the ontology in which this term exists.
`Ontology` `Term.Impl.getOntology()`
`Ontology` `RemoteTerm.Impl.getOntology()`
`Ontology` `OntologyTerm.getOntology()` Get the remote ontology referenced by this term
`Ontology` `OntologyTerm.Impl.getOntology()`
`Ontology` `IntegerOntology.IntTerm.getOntology()`
`Ontology` `OntologyTerm.Impl.getTargetOntology()`

Methods in org.biojava.ontology with parameters of type Ontology
`OntologyTerm` `Ontology.Impl.createOntologyTerm(Ontology o)`

Constructors in org.biojava.ontology with parameters of type Ontology
`OntologyTerm.Impl(Ontology ontology, Ontology target)`
`OntologyTerm.Impl(Ontology ontology, Ontology target, Object[] synonyms)`
`RemoteTerm.Impl(Ontology ontology, Term remoteTerm, String name)`
`RemoteTerm.Impl(Ontology ontology, Term remoteTerm, String name, Object[] synonyms)`
`Term.Impl(Ontology ontology, String name)`
`Term.Impl(Ontology ontology, String name, String description)`
`Term.Impl(Ontology ontology, String name, String description, Object[] synonyms)`
`Variable.Impl(Ontology ontology, String name, String description)`
`Variable.Impl(Ontology ontology, String name, String description, Object[] synonyms)`

Uses of Ontology in org.biojava.ontology.io

Methods in org.biojava.ontology.io that return Ontology
`Ontology` `TabDelimParser.parse(BufferedReader in, OntologyFactory of)` Parse an ontology from a reader.
`Ontology` `GOParser.parseGO(BufferedReader goFile, String ontoName, String ontoDescription, OntologyFactory factory)`
`Ontology` `OboParser.parseOBO(BufferedReader oboFile, String ontoName, String ontoDescription)` Parse a OBO file and return its content as a BioJava Ontology object

Uses of Ontology in org.biojava.ontology.obo

Constructors in org.biojava.ontology.obo with parameters of type Ontology
`OboFileHandler(Ontology ontology)`

Uses of Ontology in org.biojavax.ontology

Subinterfaces of Ontology in org.biojavax.ontology
`interface` `ComparableOntology` An Ontology that can be compared to another.

Classes in org.biojavax.ontology that implement Ontology
`class` `SimpleComparableOntology` Represents an ontology that can be compared to other ontologies.

Methods in org.biojavax.ontology that return Ontology
`Ontology` `SimpleComparableTriple.getOntology()` Return the ontology in which this term exists.
`Ontology` `SimpleComparableTerm.getOntology()` Return the ontology in which this term exists.