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

Packages that use Term

Package	Description
org.biojava.nbio.ontology

Uses of Term in org.biojava.nbio.ontology

Subinterfaces of Term in org.biojava.nbio.ontology

Modifier and Type	Interface and Description
interface	OntologyTerm A term in an ontology which identifies another ontology.
interface	RemoteTerm A term in another ontology.
interface	Triple A triple in an ontology.
interface	Variable

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

Modifier and Type	Class and Description
class	AbstractTerm Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
class	IntegerOntology.IntTerm
static class	OntologyTerm.Impl Simple in-memory implementation of a remote ontology term.
static class	RemoteTerm.Impl Simple in-memory implementation of a remote ontology term.
static class	Term.Impl Simple in-memory implementation of an ontology term.
static class	Triple.Impl Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple
static class	Variable.Impl

Fields in org.biojava.nbio.ontology declared as Term

Modifier and Type	Field and Description
static Term	OntoTools.ANY
static Term	OntoTools.EQUIVALENCE
static Term	OntoTools.IS_A
static Term	OntoTools.NONE
static Term	OntoTools.PART_OF
static Term	OntoTools.PARTIAL_ORDER
static Term	OntoTools.REFLEXIVE
static Term	OntoTools.RELATION
static Term	OntoTools.SYMMETRIC
static Term	OntoTools.TRANSITIVE

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

Modifier and Type	Method and Description
Term	IntegerOntology.createTerm(String name)
Term	Ontology.createTerm(String name) Create a new term in this ontology.
Term	Ontology.Impl.createTerm(String name)
Term	IntegerOntology.createTerm(String name, String description)
Term	Ontology.createTerm(String name, String description) Create a new term in this ontology.
Term	Ontology.Impl.createTerm(String name, String description)
Term	IntegerOntology.createTerm(String name, String description, Object[] synonyms)
Term	Ontology.createTerm(String name, String description, Object[] synonyms) Create a new term in this ontology.
Term	Ontology.Impl.createTerm(String name, String description, Object[] synonyms)
Term	Triple.getObject() Return the object term of this triple.
Term	Triple.Impl.getObject()
Term	Triple.getPredicate() Return a Term which defines the type of relationship between the subject and object terms.
Term	Triple.Impl.getPredicate()
Term	RemoteTerm.getRemoteTerm() Return the imported term
Term	RemoteTerm.Impl.getRemoteTerm()
Term	Triple.getSubject() Return the subject term of this triple
Term	Triple.Impl.getSubject()
Term	IntegerOntology.getTerm(String s)
Term	Ontology.getTerm(String name) Fetch the term with the specified name.
Term	Ontology.Impl.getTerm(String name)
Term	IntegerOntology.importTerm(Term t, String name)
Term	Ontology.importTerm(Term t, String localName) Create a view of a term from another ontology.
Term	Ontology.Impl.importTerm(Term t, String name)

Methods in org.biojava.nbio.ontology that return types with arguments of type Term

Modifier and Type	Method and Description
Set<Term>	Ontology.getTerms() Return all the terms in this ontology
Set<Term>	Ontology.Impl.getTerms()

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

Modifier and Type	Method and Description
boolean	IntegerOntology.containsTriple(Term subject, Term object, Term predicate)
boolean	Ontology.containsTriple(Term subject, Term object, Term predicate) See if a triple exists in this ontology
boolean	Ontology.Impl.containsTriple(Term subject, Term object, Term predicate)
Triple	IntegerOntology.createTriple(Term subject, Term object, Term predicate, String name, String description)
Triple	Ontology.createTriple(Term subject, Term object, Term predicate, String name, String description) Creates a new Triple.
Triple	Ontology.Impl.createTriple(Term subject, Term object, Term predicate, String name, String description)
void	IntegerOntology.deleteTerm(Term t)
void	Ontology.deleteTerm(Term t) Remove a term from an ontology, together with all triples which refer to it.
void	Ontology.Impl.deleteTerm(Term t)
Set	IntegerOntology.getTriples(Term subject, Term object, Term predicate)
Set<Triple>	Ontology.getTriples(Term subject, Term object, Term predicate) Return all triples from this ontology which match the supplied pattern.
Set<Triple>	Ontology.Impl.getTriples(Term subject, Term object, Term predicate)
Term	IntegerOntology.importTerm(Term t, String name)
Term	Ontology.importTerm(Term t, String localName) Create a view of a term from another ontology.
Term	Ontology.Impl.importTerm(Term t, String name)

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

Constructor and Description
Impl(Ontology ontology, Term remoteTerm, String name)
Impl(Ontology ontology, Term remoteTerm, String name, Object[] synonyms)
Impl(Term subject, Term object, Term predicate)
Impl(Term subject, Term object, Term predicate, Object[] synonyms)
Impl(Term subject, Term object, Term predicate, String name, String description)
Impl(Term subject, Term object, Term predicate, String name, String description, Object[] synonyms)