Package org.biojava.nbio.ontology

Class OntoTools

java.lang.Object

org.biojava.nbio.ontology.OntoTools

public final class OntoTools
extends Object

Tools for manipulating ontologies.

Author:

Matthew Pocock

Field Summary

Fields

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

Method Summary

Modifier and Type	Method	Description
static Ontology	getCoreOntology()	Get the Ontology that defines our core "central dogma".
static OntologyFactory	getDefaultFactory()
static IntegerOntology	getIntegerOntology()	Get the Ontology that defines integers.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

RELATION

public static final Term RELATION

ANY

public static final Term ANY

NONE

public static final Term NONE

IS_A

public static final Term IS_A

PART_OF

public static final Term PART_OF

REFLEXIVE

public static final Term REFLEXIVE

SYMMETRIC

public static final Term SYMMETRIC

TRANSITIVE

public static final Term TRANSITIVE

EQUIVALENCE

public static final Term EQUIVALENCE

PARTIAL_ORDER

public static final Term PARTIAL_ORDER

Method Details

getCoreOntology

public static Ontology getCoreOntology()

Get the Ontology that defines our core "central dogma".

This contains definitions that we have to have, such as any, predicate, is-a and transient. These are our axioms, upon which the default interpreters build.

Returns:

the "core" Ontology

getIntegerOntology

public static IntegerOntology getIntegerOntology()

Get the Ontology that defines integers.

This contains a term for each and every integer. I haven't decided yet if it contains terms for arithmatic.

Returns:

the integer Ontology

getDefaultFactory

public static OntologyFactory getDefaultFactory()