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

Packages that use Ontology

Package	Description
org.biojava.nbio.ontology
org.biojava.nbio.ontology.io	Tools for loading and saving ontologies.
org.biojava.nbio.ontology.obo

Uses of Ontology in org.biojava.nbio.ontology

Classes in org.biojava.nbio.ontology that implement Ontology

Modifier and Type	Class	Description
class	IntegerOntology
static final class	Ontology.Impl	A basic in-memory implementation of an ontology

Methods in org.biojava.nbio.ontology that return Ontology

Modifier and Type	Method	Description
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	IntegerOntology.IntTerm.getOntology()
Ontology	OntologyTerm.getOntology()	Get the remote ontology referenced by this term
Ontology	OntologyTerm.Impl.getOntology()
Ontology	RemoteTerm.Impl.getOntology()
Ontology	Term.getOntology()	Return the ontology in which this term exists.
Ontology	Term.Impl.getOntology()
Ontology	Triple.Impl.getOntology()
Ontology	OntologyTerm.Impl.getTargetOntology()

Methods in org.biojava.nbio.ontology with parameters of type Ontology

Modifier and Type	Method	Description
OntologyTerm	Ontology.Impl.createOntologyTerm(Ontology o)

Constructors in org.biojava.nbio.ontology with parameters of type Ontology

Modifier	Constructor	Description
	Impl(Ontology ontology, Ontology target)
	Impl(Ontology ontology, Ontology target, Object[] synonyms)
	Impl(Ontology ontology, Term remoteTerm, String name)
	Impl(Ontology ontology, Term remoteTerm, String name, Object[] synonyms)
	Impl(Ontology ontology, String name)
	Impl(Ontology ontology, String name, String description)
	Impl(Ontology ontology, String name, String description, Object[] synonyms)
	Impl(Ontology ontology, String name, String description)
	Impl(Ontology ontology, String name, String description, Object[] synonyms)

Uses of Ontology in org.biojava.nbio.ontology.io

Methods in org.biojava.nbio.ontology.io that return Ontology

Modifier and Type	Method	Description
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.nbio.ontology.obo

Constructors in org.biojava.nbio.ontology.obo with parameters of type Ontology

Modifier	Constructor	Description
	OboFileHandler(Ontology ontology)