com.clarkparsia.owlapiv3

Class OntologyUtils

java.lang.Object

com.clarkparsia.owlapiv3.OntologyUtils

public class OntologyUtils
extends Object

Title:

Description:

Copyright: Copyright (c) 2007

Company: Clark & Parsia, LLC.

Author:

Evren Sirin

Constructor Summary

Constructors

Constructor and Description
OntologyUtils()

Method Summary

Modifier and Type	Method and Description
static void	addAxiom(org.semanticweb.owlapi.model.OWLAxiom axiom, Set<org.semanticweb.owlapi.model.OWLOntology> ontologies, org.semanticweb.owlapi.model.OWLOntologyManager manager) Add the axiom to all the given ontologies.
static void	addAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, Collection<? extends org.semanticweb.owlapi.model.OWLAxiom> axioms)
static void	addAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLAxiom... axioms)
static void	clearOWLOntologyManager()
static boolean	containsClass(Set<Set<org.semanticweb.owlapi.model.OWLClass>> classes, org.semanticweb.owlapi.model.OWLClass cls)
static boolean	containsUnreferencedEntity(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLClassExpression desc) Determines if a class description contains any unreferenced entities with respect to the ontology that contains the entailments which are being explained.
static org.semanticweb.owlapi.model.OWLEntity	findEntity(String name, org.semanticweb.owlapi.model.OWLOntology ontology) Finds an entity (class, individual, object or data property) in the given ontology that has the given local name or URI.
static org.semanticweb.owlapi.model.OWLEntity	findEntity(String name, Set<org.semanticweb.owlapi.model.OWLOntology> ontologies) Finds an entity (class, individual, object or data property) in the given set of ontologies that has the given local name or URI.
static org.semanticweb.owlapi.model.OWLOntologyManager	getOWLOntologyManager()
static Set<org.semanticweb.owlapi.model.OWLEntity>	getSignature(org.semanticweb.owlapi.model.OWLAxiom axiom) Given an axiom, return its signature.
static Set<org.semanticweb.owlapi.model.OWLAxiom>	loadAxioms(InputStream inputStream) Loads the axioms from the given stream
static org.semanticweb.owlapi.model.OWLOntology	loadOntology(InputStream inputStream) Loads the ontology from the given stream
static org.semanticweb.owlapi.model.OWLOntology	loadOntology(InputStream inputStream, boolean withAnnotations) Loads the ontology with given URI and optionally removes all annotations leaving only logical axioms.
static org.semanticweb.owlapi.model.OWLOntology	loadOntology(String uri) Loads the ontology with given URI.
static org.semanticweb.owlapi.model.OWLOntology	loadOntology(String uri, boolean withAnnotations) Loads the ontology with given URI and optionally removes all annotations leaving only logical axioms.
static void	printAxioms(Collection<? extends org.semanticweb.owlapi.model.OWLAxiom> axioms) Prints a set of axioms to console
static void	printOntology(org.semanticweb.owlapi.model.OWLOntology ont) Prints an ontology to console
static void	removeAllAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLOntologyManager manager) Removes all annotations (non-logical axioms) but not declarations from the ontology causing the ontology to be changed in an unreversible way.
static Set<org.semanticweb.owlapi.model.OWLOntology>	removeAxiom(org.semanticweb.owlapi.model.OWLAxiom axiom, Set<org.semanticweb.owlapi.model.OWLOntology> ontologies, org.semanticweb.owlapi.model.OWLOntologyManager manager) Removes an axiom from all the given ontologies that contains the axiom and returns those ontologies.
static void	removeAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, Collection<? extends org.semanticweb.owlapi.model.OWLAxiom> axioms)
static void	removeAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLAxiom... axioms)
static void	save(org.semanticweb.owlapi.model.OWLOntology ont, String path)
static void	updateOntology(org.semanticweb.owlapi.model.OWLOntology ontology, Iterable<? extends org.semanticweb.owlapi.model.OWLAxiom> additions, Iterable<? extends org.semanticweb.owlapi.model.OWLAxiom> removals) Update the ontology by adding and/or removing the given set of axioms

Methods inherited from class java.lang.Object

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

Constructor Detail

OntologyUtils

public OntologyUtils()

Method Detail

addAxioms

public static void addAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                             Collection<? extends org.semanticweb.owlapi.model.OWLAxiom> axioms)

addAxioms

public static void addAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                             org.semanticweb.owlapi.model.OWLAxiom... axioms)

containsClass

public static boolean containsClass(Set<Set<org.semanticweb.owlapi.model.OWLClass>> classes,
                                    org.semanticweb.owlapi.model.OWLClass cls)

getSignature

public static Set<org.semanticweb.owlapi.model.OWLEntity> getSignature(org.semanticweb.owlapi.model.OWLAxiom axiom)

Given an axiom, return its signature.

getOWLOntologyManager

public static org.semanticweb.owlapi.model.OWLOntologyManager getOWLOntologyManager()

clearOWLOntologyManager

public static void clearOWLOntologyManager()

loadOntology

public static org.semanticweb.owlapi.model.OWLOntology loadOntology(String uri)

Loads the ontology with given URI.

Parameters:

uri - the ontology uri

Returns:

the ontology

loadOntology

public static org.semanticweb.owlapi.model.OWLOntology loadOntology(InputStream inputStream)

Loads the ontology from the given stream

loadAxioms

public static Set<org.semanticweb.owlapi.model.OWLAxiom> loadAxioms(InputStream inputStream)

Loads the axioms from the given stream

loadOntology

public static org.semanticweb.owlapi.model.OWLOntology loadOntology(String uri,
                                                                    boolean withAnnotations)

Loads the ontology with given URI and optionally removes all annotations leaving only logical axioms.

Parameters:

uri - the ontology uri

withAnnotations - if false removes all annotation axioms from the ontology, otherwise leaves the ontology intact

Returns:

the ontology

See Also:

removeAllAnnotations(OWLOntology, OWLOntologyManager)

loadOntology

public static org.semanticweb.owlapi.model.OWLOntology loadOntology(InputStream inputStream,
                                                                    boolean withAnnotations)

Loads the ontology with given URI and optionally removes all annotations leaving only logical axioms.

Parameters:

inputStream - input stream

withAnnotations - if false removes all annotation axioms from the ontology, otherwise leaves the ontology intact

Returns:

the ontology

See Also:

removeAllAnnotations(OWLOntology, OWLOntologyManager)

printAxioms

public static void printAxioms(Collection<? extends org.semanticweb.owlapi.model.OWLAxiom> axioms)

Prints a set of axioms to console

printOntology

public static void printOntology(org.semanticweb.owlapi.model.OWLOntology ont)

Prints an ontology to console

removeAxioms

public static void removeAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                Collection<? extends org.semanticweb.owlapi.model.OWLAxiom> axioms)

removeAxioms

public static void removeAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                org.semanticweb.owlapi.model.OWLAxiom... axioms)

save

public static void save(org.semanticweb.owlapi.model.OWLOntology ont,
                        String path)
                 throws org.semanticweb.owlapi.model.OWLOntologyStorageException

Throws:

org.semanticweb.owlapi.model.OWLOntologyStorageException

updateOntology

public static void updateOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                  Iterable<? extends org.semanticweb.owlapi.model.OWLAxiom> additions,
                                  Iterable<? extends org.semanticweb.owlapi.model.OWLAxiom> removals)

Update the ontology by adding and/or removing the given set of axioms

containsUnreferencedEntity

public static boolean containsUnreferencedEntity(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                 org.semanticweb.owlapi.model.OWLClassExpression desc)

Determines if a class description contains any unreferenced entities with respect to the ontology that contains the entailments which are being explained.

Parameters:

desc - The description to be searched

Returns:

true if the description references entities that the ontology that contains entailments which are being explained, otherwise false

removeAxiom

public static Set<org.semanticweb.owlapi.model.OWLOntology> removeAxiom(org.semanticweb.owlapi.model.OWLAxiom axiom,
                                                                        Set<org.semanticweb.owlapi.model.OWLOntology> ontologies,
                                                                        org.semanticweb.owlapi.model.OWLOntologyManager manager)

Removes an axiom from all the given ontologies that contains the axiom and returns those ontologies.

Parameters:

axiom - axiom being removed

ontologies - ontologies from which axiom is being removed

manager - manager to apply the actual change

Returns:

set of ontologies that have been affected

addAxiom

public static void addAxiom(org.semanticweb.owlapi.model.OWLAxiom axiom,
                            Set<org.semanticweb.owlapi.model.OWLOntology> ontologies,
                            org.semanticweb.owlapi.model.OWLOntologyManager manager)

Add the axiom to all the given ontologies.

Parameters:

axiom -

ontologies -

manager -

removeAllAnnotations

public static void removeAllAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology,
                                        org.semanticweb.owlapi.model.OWLOntologyManager manager)

Removes all annotations (non-logical axioms) but not declarations from the ontology causing the ontology to be changed in an unreversible way. For any entity that is only referenced in an annotation but no logical axiom a declaration is added so that the referenced entities by the ontology remain same. Annotations have no semantic importance and can be ignored for reasoning purposes including generating explanations and computing modules. Removing them from the ontology completely reduces the memory requirements which is very high for large-scale annotation-heavy ontologies.

Parameters:

ontology - the ontology being changed

findEntity

public static org.semanticweb.owlapi.model.OWLEntity findEntity(String name,
                                                                Set<org.semanticweb.owlapi.model.OWLOntology> ontologies)

Finds an entity (class, individual, object or data property) in the given set of ontologies that has the given local name or URI.

Parameters:

name - URI or local name for an entity

ontologies - ontologies we are searching

Returns:

an entity referenced in the given ontology that has the given URI or local name

See Also:

findEntity(String, OWLOntology)

findEntity

public static org.semanticweb.owlapi.model.OWLEntity findEntity(String name,
                                                                org.semanticweb.owlapi.model.OWLOntology ontology)

Finds an entity (class, individual, object or data property) in the given ontology that has the given local name or URI. If the given name is not an absolute URI we use the logical URI of the ontology as the namespace and search for an entity with that URI. If the URI is punned in the ontology , e.g. used both as a class and as an individual, any one of the punned entities may be returned.

Parameters:

name - URI or local name for an entity

ontology - ontology we are searching

Returns:

an entity referenced in the given ontology that has the given URI or local name