org.semanticweb.owlapi.model

Interface OWLOntology

All Superinterfaces:

Comparable<OWLObject>, HasAnnotationPropertiesInSignature, HasAnnotations, HasAnonymousIndividuals, HasAxioms, HasAxiomsByType, HasClassesInSignature, HasContainsAxiom, HasContainsEntityInSignature, HasDataPropertiesInSignature, HasDatatypesInSignature, HasDirectImports, HasGetEntitiesInSignature, HasImportsClosure, HasIndividualsInSignature, HasLogicalAxioms, HasObjectPropertiesInSignature, HasOntologyID, HasSignature, IsAnonymous, OWLAxiomCollection, OWLAxiomCollectionBooleanArgs, OWLAxiomCollectionNoArgs, OWLAxiomIndex, OWLObject, OWLSignature, OWLSignatureBooleanArgs, Serializable

All Known Subinterfaces:

OWLMutableOntology

All Known Implementing Classes:

ConcurrentOWLOntologyImpl, OWLImmutableOntologyImpl, OWLOntologyImpl

public interface OWLOntology
extends OWLObject, HasAnnotations, HasDirectImports, HasImportsClosure, HasOntologyID, OWLAxiomCollection, OWLAxiomCollectionBooleanArgs, OWLAxiomCollectionNoArgs, OWLSignature, OWLSignatureBooleanArgs, OWLAxiomIndex

Represents an OWL 2 Ontology in the OWL 2 specification.
An OWLOntology consists of a possibly empty set of OWLAxioms and a possibly empty set of OWLAnnotations. An ontology can have an ontology IRI which can be used to identify the ontology. If it has an ontology IRI then it may also have an ontology version IRI. Since OWL 2, an ontology need not have an ontology IRI. (See the OWL 2 Structural Specification An ontology cannot be modified directly. Changes must be applied via its OWLOntologyManager.

Since:

2.0.0

Author:

Matthew Horridge, The University Of Manchester, Bio-Health Informatics Group

Method Summary

Modifier and Type	Method and Description
void	accept(OWLNamedObjectVisitor visitor) accept for named object visitor
<O> O	accept(OWLNamedObjectVisitorEx<O> visitor) Accepts a visitor
default boolean	containsEntitiesOfTypeInSignature(EntityType<?> type, Imports includeImportsClosure) Determine whether the instance has entities of the specified type in its signature or in its import closure - e.g., whether an ontology has classes, object propertyies, or named individuals in its signature.
Set<OWLAxiom>	getABoxAxioms(Imports includeImportsClosure) Gets the axioms that form the ABox for this ontology, i.e., the ones whose type is in the AxiomType::ABoxAxiomTypes.
Set<OWLAnnotation>	getAnnotations() Gets the annotations on this ontology.
Set<OWLOntology>	getDirectImports() Gets the set of loaded ontologies that this ontology is related to via the directlyImports relation.
Set<IRI>	getDirectImportsDocuments() Gets the set of document IRIs that are directly imported by this ontology.
Set<OWLClassAxiom>	getGeneralClassAxioms() Gets the set of general axioms in this ontology.
Set<OWLOntology>	getImports() Gets the set of loaded ontologies that this ontology is related to via the transitive closure of the directlyImports relation. For example, if this ontology imports ontology B, and ontology B imports ontology C, then this method will return the set consisting of ontology B and ontology C.
Set<OWLOntology>	getImportsClosure() Gets the set of loaded ontologies that this ontology is related to via the reflexive transitive closure of the directlyImports relation as defined in Section 3.4 of the OWL 2 Structural Specification.
Set<OWLImportsDeclaration>	getImportsDeclarations() Gets the set of imports declarations for this ontology.
OWLOntologyID	getOntologyID() Gets the identity of this ontology (i.e.
OWLOntologyManager	getOWLOntologyManager() Gets the manager that manages this ontology.
Set<OWLAxiom>	getRBoxAxioms(Imports includeImportsClosure) Gets the axioms that form the RBox for this ontology, i.e., the ones whose type is in the AxiomType::RBoxAxiomTypes.
Set<OWLEntity>	getSignature() Gets the entities that are in the signature of this ontology.
Set<OWLEntity>	getSignature(Imports includeImportsClosure) Gets the entities that are in the signature of this ontology.
Set<OWLAxiom>	getTBoxAxioms(Imports includeImportsClosure) Gets the axioms that form the TBox for this ontology, i.e., the ones whose type is in the AxiomType::TBoxAxiomTypes.
boolean	isDeclared(OWLEntity owlEntity) Determines if this ontology declares an entity i.e.
boolean	isDeclared(OWLEntity owlEntity, Imports includeImportsClosure) Determines if this ontology or its imports closure declares an entity i.e.
boolean	isEmpty() Determines if this ontology is empty - an ontology is empty if it does not contain any axioms (i.e.
void	saveOntology() Saves the ontology.
void	saveOntology(IRI documentIRI) Saves the ontology, using the specified document IRI to determine where/how the ontology should be saved.
void	saveOntology(OutputStream outputStream) Saves the ontology, to the specified output stream
void	saveOntology(OWLDocumentFormat ontologyFormat) Saves the ontology in the specified ontology format to its document URI.
void	saveOntology(OWLDocumentFormat ontologyFormat, IRI documentIRI) Saves the ontology to the specified document IRI in the specified ontology format.
void	saveOntology(OWLDocumentFormat ontologyFormat, OutputStream outputStream) Saves the ontology to the specified output stream in the specified ontology format.
void	saveOntology(OWLDocumentFormat ontologyFormat, OWLOntologyDocumentTarget documentTarget) Saves the ontology to the specified output target in the specified ontology format.
void	saveOntology(OWLOntologyDocumentTarget documentTarget) Saves the ontology to the specified OWLOntologyDocumentTarget.
void	setOWLOntologyManager(OWLOntologyManager manager) Sets the manager for this ontology.

Methods inherited from interface org.semanticweb.owlapi.model.OWLObject

accept, accept, getNestedClassExpressions, isBottomEntity, isIndividual, isIRI, isTopEntity, toString

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface org.semanticweb.owlapi.model.HasAnonymousIndividuals

getAnonymousIndividuals

Methods inherited from interface org.semanticweb.owlapi.model.IsAnonymous

isAnonymous, isNamed

Methods inherited from interface org.semanticweb.owlapi.model.OWLAxiomCollection

containsAxiom, getAxiomCount, getAxiomCount, getAxioms, getAxioms, getAxioms, getAxioms, getAxioms, getAxioms, getAxioms, getAxioms, getAxiomsIgnoreAnnotations, getLogicalAxiomCount, getLogicalAxioms, getReferencingAxioms

Methods inherited from interface org.semanticweb.owlapi.model.OWLAxiomCollectionBooleanArgs

containsAxiom, containsAxiomIgnoreAnnotations, getAxiomCount, getAxiomCount, getAxioms, getAxioms, getAxioms, getAxioms, getAxioms, getAxioms, getAxioms, getAxioms, getAxiomsIgnoreAnnotations, getLogicalAxiomCount, getLogicalAxioms, getReferencingAxioms

Methods inherited from interface org.semanticweb.owlapi.model.OWLAxiomCollectionNoArgs

containsAxiomIgnoreAnnotations, getAxiomCount, getAxiomCount, getAxioms, getAxioms, getAxioms, getAxioms, getAxioms, getAxioms, getAxiomsIgnoreAnnotations, getLogicalAxiomCount, getReferencingAxioms

Methods inherited from interface org.semanticweb.owlapi.model.HasAxioms

getAxioms

Methods inherited from interface org.semanticweb.owlapi.model.HasLogicalAxioms

getLogicalAxioms

Methods inherited from interface org.semanticweb.owlapi.model.HasAxiomsByType

getAxioms

Methods inherited from interface org.semanticweb.owlapi.model.HasContainsAxiom

containsAxiom

Methods inherited from interface org.semanticweb.owlapi.model.OWLSignature

containsAnnotationPropertyInSignature, containsAnnotationPropertyInSignature, containsClassInSignature, containsClassInSignature, containsDataPropertyInSignature, containsDataPropertyInSignature, containsDatatypeInSignature, containsDatatypeInSignature, containsEntitiesOfTypeInSignature, containsEntityInSignature, containsEntityInSignature, containsEntityInSignature, containsIndividualInSignature, containsIndividualInSignature, containsObjectPropertyInSignature, containsObjectPropertyInSignature, containsReference, containsReference, getAnnotationPropertiesInSignature, getClassesInSignature, getDataPropertiesInSignature, getDatatypesInSignature, getEntitiesInSignature, getIndividualsInSignature, getObjectPropertiesInSignature, getPunnedIRIs, getReferencedAnonymousIndividuals

Methods inherited from interface org.semanticweb.owlapi.model.HasAnnotationPropertiesInSignature

getAnnotationPropertiesInSignature

Methods inherited from interface org.semanticweb.owlapi.model.OWLSignatureBooleanArgs

containsAnnotationPropertyInSignature, containsClassInSignature, containsDataPropertyInSignature, containsDatatypeInSignature, containsEntityInSignature, containsEntityInSignature, containsIndividualInSignature, containsObjectPropertyInSignature, containsReference, getAnnotationPropertiesInSignature, getClassesInSignature, getDataPropertiesInSignature, getDatatypesInSignature, getEntitiesInSignature, getIndividualsInSignature, getObjectPropertiesInSignature, getReferencedAnonymousIndividuals

Methods inherited from interface org.semanticweb.owlapi.model.HasGetEntitiesInSignature

getEntitiesInSignature

Methods inherited from interface org.semanticweb.owlapi.model.HasClassesInSignature

getClassesInSignature

Methods inherited from interface org.semanticweb.owlapi.model.HasObjectPropertiesInSignature

getObjectPropertiesInSignature

Methods inherited from interface org.semanticweb.owlapi.model.HasDataPropertiesInSignature

getDataPropertiesInSignature

Methods inherited from interface org.semanticweb.owlapi.model.HasDatatypesInSignature

getDatatypesInSignature

Methods inherited from interface org.semanticweb.owlapi.model.HasIndividualsInSignature

getIndividualsInSignature

Methods inherited from interface org.semanticweb.owlapi.model.HasContainsEntityInSignature

containsEntityInSignature

Methods inherited from interface org.semanticweb.owlapi.model.OWLAxiomIndex

contains, filterAxioms, getAnnotationAssertionAxioms, getAnnotationPropertyDomainAxioms, getAnnotationPropertyRangeAxioms, getAsymmetricObjectPropertyAxioms, getAxioms, getAxioms, getClassAssertionAxioms, getClassAssertionAxioms, getDataPropertyAssertionAxioms, getDataPropertyDomainAxioms, getDataPropertyRangeAxioms, getDataSubPropertyAxiomsForSubProperty, getDataSubPropertyAxiomsForSuperProperty, getDatatypeDefinitions, getDeclarationAxioms, getDifferentIndividualAxioms, getDisjointClassesAxioms, getDisjointDataPropertiesAxioms, getDisjointObjectPropertiesAxioms, getDisjointUnionAxioms, getEquivalentClassesAxioms, getEquivalentDataPropertiesAxioms, getEquivalentObjectPropertiesAxioms, getFunctionalDataPropertyAxioms, getFunctionalObjectPropertyAxioms, getHasKeyAxioms, getInverseFunctionalObjectPropertyAxioms, getInverseObjectPropertyAxioms, getIrreflexiveObjectPropertyAxioms, getNegativeDataPropertyAssertionAxioms, getNegativeObjectPropertyAssertionAxioms, getObjectPropertyAssertionAxioms, getObjectPropertyDomainAxioms, getObjectPropertyRangeAxioms, getObjectSubPropertyAxiomsForSubProperty, getObjectSubPropertyAxiomsForSuperProperty, getReflexiveObjectPropertyAxioms, getSameIndividualAxioms, getSubAnnotationPropertyOfAxioms, getSubClassAxiomsForSubClass, getSubClassAxiomsForSuperClass, getSymmetricObjectPropertyAxioms, getTransitiveObjectPropertyAxioms

Method Detail

accept

void accept(@Nonnull
            OWLNamedObjectVisitor visitor)

accept for named object visitor

Parameters:

visitor - the visitor

accept

@Nonnull
<O> O accept(@Nonnull
                      OWLNamedObjectVisitorEx<O> visitor)

Accepts a visitor

Type Parameters:

O - visitor return type

Parameters:

visitor - The visitor

Returns:

visitor return value

getOWLOntologyManager

@Nonnull
OWLOntologyManager getOWLOntologyManager()

Gets the manager that manages this ontology. The manager is used by various methods on OWLOntology to resolve imports

Returns:

The manager for this ontology.

setOWLOntologyManager

void setOWLOntologyManager(OWLOntologyManager manager)

Sets the manager for this ontology. This method is used when moving ontologies from one manager to another and when removing an ontology form a manager, and should be used by OWLOntologyManager implementations only.

Parameters:

manager - the new manager for this ontology

getOntologyID

@Nonnull
OWLOntologyID getOntologyID()

Gets the identity of this ontology (i.e. ontology IRI + version IRI).

Specified by:

getOntologyID in interface HasOntologyID

Returns:

The ID of this ontology.

getAnnotations

@Nonnull
Set<OWLAnnotation> getAnnotations()

Gets the annotations on this ontology.

Specified by:

getAnnotations in interface HasAnnotations

Returns:

A set of annotations on this ontology. The set returned will be a copy - modifying the set will have no effect on the annotations in this ontology, similarly, any changes that affect the annotations on this ontology will not change the returned set.

getDirectImportsDocuments

@Nonnull
Set<IRI> getDirectImportsDocuments()

Gets the set of document IRIs that are directly imported by this ontology. This corresponds to the IRIs defined by the directlyImportsDocument association as discussed in Section 3.4 of the OWL 2 Structural specification.

Returns:

The set of directly imported IRIs.

Throws:

UnknownOWLOntologyException - If this ontology is no longer managed by its manager because it was removed from the manager.

getDirectImports

@Nonnull
Set<OWLOntology> getDirectImports()

Gets the set of loaded ontologies that this ontology is related to via the directlyImports relation. See Section 3.4 of the OWL 2 specification for the definition of the directlyImports relation.
Note that there may be fewer ontologies in the set returned by this method than there are IRIs in the set returned by the getDirectImportsDocuments() method. This will be the case if some of the ontologies that are directly imported by this ontology are not loaded for what ever reason.

Specified by:

getDirectImports in interface HasDirectImports

Returns:

A set of ontologies such that for this ontology O, and each ontology O' in the set, (O, O') is in the directlyImports relation.

Throws:

UnknownOWLOntologyException - If this ontology is no longer managed by its manager because it was removed from the manager.

getImports

@Nonnull
Set<OWLOntology> getImports()

Gets the set of loaded ontologies that this ontology is related to via the transitive closure of the directlyImports relation.
For example, if this ontology imports ontology B, and ontology B imports ontology C, then this method will return the set consisting of ontology B and ontology C.

Returns:

The set of ontologies that this ontology is related to via the transitive closure of the directlyImports relation. The set that is returned is a copy - it will not be updated if the ontology changes. It is therefore safe to apply changes to this ontology while iterating over this set.

Throws:

UnknownOWLOntologyException - if this ontology is no longer managed by its manager because it was removed from the manager.

getImportsClosure

@Nonnull
Set<OWLOntology> getImportsClosure()

Gets the set of loaded ontologies that this ontology is related to via the reflexive transitive closure of the directlyImports relation as defined in Section 3.4 of the OWL 2 Structural Specification. (i.e. The set returned includes all ontologies returned by the getImports() method plus this ontology.)
For example, if this ontology imports ontology B, and ontology B imports ontology C, then this method will return the set consisting of this ontology, ontology B and ontology C.

Specified by:

getImportsClosure in interface HasImportsClosure

Returns:

The set of ontologies in the reflexive transitive closure of the directlyImports relation.

Throws:

UnknownOWLOntologyException - If this ontology is no longer managed by its manager because it was removed from the manager.

containsEntitiesOfTypeInSignature

default boolean containsEntitiesOfTypeInSignature(EntityType<?> type,
                                                  Imports includeImportsClosure)

Description copied from interface: OWLSignature

Determine whether the instance has entities of the specified type in its signature or in its import closure - e.g., whether an ontology has classes, object propertyies, or named individuals in its signature. Anonymous individuals are not included.

Specified by:

containsEntitiesOfTypeInSignature in interface OWLSignature

Parameters:

type - type of entity to check

includeImportsClosure - if INCLUDED, include imports closure.

Returns:

true if entities of the specified type are in the signature

getImportsDeclarations

@Nonnull
Set<OWLImportsDeclaration> getImportsDeclarations()

Gets the set of imports declarations for this ontology. The set returned represents the set of IRIs that correspond to the set of IRIs in an ontology's directlyImportsDocuments (see Section 3 in the OWL 2 structural specification).

Returns:

The set of imports declarations that correspond to the set of ontology document IRIs that are directly imported by this ontology. The set that is returned is a copy - it will not be updated if the ontology changes. It is therefore safe to apply changes to this ontology while iterating over this set.

isEmpty

boolean isEmpty()

Determines if this ontology is empty - an ontology is empty if it does not contain any axioms (i.e. HasAxioms.getAxioms() returns the empty set), and it does not have any annotations (i.e. getAnnotations() returns the empty set).

Returns:

true if the ontology is empty, otherwise false.

getTBoxAxioms

@Nonnull
Set<OWLAxiom> getTBoxAxioms(@Nonnull
                                     Imports includeImportsClosure)

Gets the axioms that form the TBox for this ontology, i.e., the ones whose type is in the AxiomType::TBoxAxiomTypes.

Parameters:

includeImportsClosure - if INCLUDED, the imports closure is included.

Returns:

A set containing the axioms which are of the specified type. The set that is returned is a copy of the axioms in the ontology (and its imports closure) - it will not be updated if the ontology changes.

getABoxAxioms

@Nonnull
Set<OWLAxiom> getABoxAxioms(@Nonnull
                                     Imports includeImportsClosure)

Gets the axioms that form the ABox for this ontology, i.e., the ones whose type is in the AxiomType::ABoxAxiomTypes.

Parameters:

includeImportsClosure - if INCLUDED, the imports closure is included.

Returns:

A set containing the axioms which are of the specified type. The set that is returned is a copy of the axioms in the ontology (and its imports closure) - it will not be updated if the ontology changes.

getRBoxAxioms

@Nonnull
Set<OWLAxiom> getRBoxAxioms(@Nonnull
                                     Imports includeImportsClosure)

Gets the axioms that form the RBox for this ontology, i.e., the ones whose type is in the AxiomType::RBoxAxiomTypes.

Parameters:

includeImportsClosure - if INCLUDED, the imports closure is included.

Returns:

A set containing the axioms which are of the specified type. The set that is returned is a copy of the axioms in the ontology (and its imports closure) - it will not be updated if the ontology changes.

getGeneralClassAxioms

@Nonnull
Set<OWLClassAxiom> getGeneralClassAxioms()

Gets the set of general axioms in this ontology. This includes:

• Subclass axioms that have a complex class as the subclass
• Equivalent class axioms that don't contain any named classes ( OWLClasses)
• Disjoint class axioms that don't contain any named classes ( OWLClasses)

Returns:

The set that is returned is a copy of the axioms in the ontology - it will not be updated if the ontology changes. It is therefore safe to apply changes to this ontology while iterating over this set.

getSignature

@Nonnull
Set<OWLEntity> getSignature()

Gets the entities that are in the signature of this ontology. The signature of an ontology is the set of entities that are used to build axioms and annotations in the ontology. (See The OWL 2 Structural Specification)

Specified by:

getSignature in interface HasSignature

Returns:

A set of OWLEntity objects. The set that is returned is a copy - it will not be updated if the ontology changes. It is therefore safe to apply changes to this ontology while iterating over this set.

See Also:

HasClassesInSignature.getClassesInSignature(), HasObjectPropertiesInSignature.getObjectPropertiesInSignature(), HasDataPropertiesInSignature.getDataPropertiesInSignature(), HasIndividualsInSignature.getIndividualsInSignature()

getSignature

@Nonnull
Set<OWLEntity> getSignature(@Nonnull
                                     Imports includeImportsClosure)

Gets the entities that are in the signature of this ontology. The signature of an ontology is the set of entities that are used to build axioms and annotations in the ontology. (See The OWL 2 Structural Specification)

Parameters:

includeImportsClosure - if INCLUDED, the imports closure is included.

Returns:

A set of OWLEntity objects. The set that is returned is a copy - it will not be updated if the ontology changes. It is therefore safe to apply changes to this ontology while iterating over this set.

See Also:

HasClassesInSignature.getClassesInSignature(), HasObjectPropertiesInSignature.getObjectPropertiesInSignature(), HasDataPropertiesInSignature.getDataPropertiesInSignature(), HasIndividualsInSignature.getIndividualsInSignature()

isDeclared

boolean isDeclared(@Nonnull
                   OWLEntity owlEntity)

Determines if this ontology declares an entity i.e. it contains a declaration axiom for the specified entity.

Parameters:

owlEntity - The entity to be tested for

Returns:

true if the ontology contains a declaration for the specified entity, otherwise false.

isDeclared

boolean isDeclared(@Nonnull
                   OWLEntity owlEntity,
                   @Nonnull
                   Imports includeImportsClosure)

Determines if this ontology or its imports closure declares an entity i.e. contains a declaration axiom for the specified entity.

Parameters:

owlEntity - The entity to be tested for

includeImportsClosure - if INCLUDED, the imports closure is included.

Returns:

true if the ontology or its imports closure contains a declaration for the specified entity, otherwise false.

saveOntology

void saveOntology()
           throws OWLOntologyStorageException

Saves the ontology. The ontology will be saved to the location that it was loaded from, or if it was created programmatically, it will be saved to the location specified by an ontology IRI mapper at creation time. The ontology will be saved in the same format which it was loaded from, or the default ontology format if the ontology was created programmatically.

Throws:

OWLOntologyStorageException - An exception will be thrown if there is a problem with saving the ontology, or the ontology can't be saved in the format it was loaded from.

saveOntology

void saveOntology(@Nonnull
                  IRI documentIRI)
           throws OWLOntologyStorageException

Saves the ontology, using the specified document IRI to determine where/how the ontology should be saved.

Parameters:

documentIRI - The document IRI where the ontology should be saved to

Throws:

OWLOntologyStorageException - If the ontology cannot be saved

saveOntology

void saveOntology(@Nonnull
                  OutputStream outputStream)
           throws OWLOntologyStorageException

Saves the ontology, to the specified output stream

Parameters:

outputStream - The output stream where the ontology will be saved to

Throws:

OWLOntologyStorageException - If there was a problem saving this ontology to the specified output stream

saveOntology

void saveOntology(@Nonnull
                  OWLDocumentFormat ontologyFormat)
           throws OWLOntologyStorageException

Saves the ontology in the specified ontology format to its document URI.

Parameters:

ontologyFormat - The format in which the ontology should be saved.

Throws:

OWLOntologyStorageException - If the ontology cannot be saved.

saveOntology

void saveOntology(@Nonnull
                  OWLDocumentFormat ontologyFormat,
                  @Nonnull
                  IRI documentIRI)
           throws OWLOntologyStorageException

Saves the ontology to the specified document IRI in the specified ontology format.

Parameters:

ontologyFormat - The format in which to save the ontology

documentIRI - The document IRI where the ontology should be saved to

Throws:

OWLOntologyStorageException - If the ontology could not be saved.

saveOntology

void saveOntology(@Nonnull
                  OWLDocumentFormat ontologyFormat,
                  @Nonnull
                  OutputStream outputStream)
           throws OWLOntologyStorageException

Saves the ontology to the specified output stream in the specified ontology format.

Parameters:

ontologyFormat - The format in which to save the ontology

outputStream - The output stream where the ontology will be saved to.

Throws:

OWLOntologyStorageException - If the ontology could not be saved.

saveOntology

void saveOntology(@Nonnull
                  OWLOntologyDocumentTarget documentTarget)
           throws OWLOntologyStorageException

Saves the ontology to the specified OWLOntologyDocumentTarget.

Parameters:

documentTarget - The output target where the ontology will be saved to.

Throws:

OWLOntologyStorageException - If the ontology could not be saved.

saveOntology

void saveOntology(@Nonnull
                  OWLDocumentFormat ontologyFormat,
                  @Nonnull
                  OWLOntologyDocumentTarget documentTarget)
           throws OWLOntologyStorageException

Saves the ontology to the specified output target in the specified ontology format.

Parameters:

ontologyFormat - The output format in which to save the ontology

documentTarget - The output target where the ontology will be saved to

Throws:

OWLOntologyStorageException - If the ontology could not be saved.