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## 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.

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