Ontology (GATE Core 9.1-SNAPSHOT API)

All Superinterfaces:

FeatureBearer, LanguageResource, NameBearer, Resource, Serializable
```
public interface Ontology
extends LanguageResource
```
Interface for ontology language resources. A client program may only use the methods defined in this interface to manipulate ontologies and must never use any methods from the implementing package. All ontology language resources must be created using the Factory.createResource method. See the documentation for the implementing plugins for details on how to create ontology language resources programmatically. Unless stated otherwise, this documentation describes the behavior of the methods as implemented in the ontology API implementation plugin, Ontology The backwards-compatibility plugin Ontology_OWLIM2 implements all of the deprecated methods and classes but none of the new methods that were added to the API in version 5.1. Some but not all depracated methods are also implemented in the new plugin Ontology The use of deprecated methods should be avoided and replaced by other methods as soon as possible as the backwards-compatibility plugin may get removed in the future and deprecated methods may get removed from the API.

Author:

Niraj Aswani, Johann Petrak

Method Summary

All Methods Instance Methods Abstract Methods Deprecated Methods
Modifier and Type	Method and Description
`AllValuesFromRestriction`	`addAllValuesFromRestriction(ObjectProperty onProperty, OClass theClass)`
`AllValuesFromRestriction`	`addAllValuesFromRestriction(RDFProperty onProperty, OResource hasValue)` Deprecated. - this method is deprecated and kept for backwards compatibility as long as the OntologyOWLIM2 plugin is kept. Use the method `addAllValuesFromRestriction(ObjectProperty, OClass)` instead.
`AnnotationProperty`	`addAnnotationProperty(OURI aPropertyURI)` Creates a new AnnotationProperty.
`AnonymousClass`	`addAnonymousClass()`
`CardinalityRestriction`	`addCardinalityRestriction(RDFProperty onProperty, String cardinalityValue)` Adds a new Cardinality Restriction to the ontology.
`DatatypeProperty`	`addDatatypeProperty(OURI aPropertyURI, Set<OClass> domain, DataType aDatatype)` Create a DatatypeProperty with the given domain and range.
`HasValueRestriction`	`addHasValueRestriction(RDFProperty onProperty, OResource hasValue)` Adds a new HasValue Restriction to the ontology.
`MaxCardinalityRestriction`	`addMaxCardinalityRestriction(RDFProperty onProperty, String maxCardinalityValue)` Adds a new MaxCardinality Restriction to the ontology.
`MinCardinalityRestriction`	`addMinCardinalityRestriction(RDFProperty onProperty, String minCardinalityValue)` Adds a new MinCardinality Restriction to the ontology.
`ObjectProperty`	`addObjectProperty(OURI aPropertyURI, Set<OClass> domain, Set<OClass> range)` Creates a new object property (a property that takes instances as values).
`OClass`	`addOClass(OURI aURI)` Creates a new OWL Class and adds it the ontology.
`OClass`	`addOClass(OURI aURI, byte classType)` Deprecated. - use one of the dedicated methods to add a named class or a restriction instead
`OInstance`	`addOInstance(OURI theInstanceURI, OClass theClass)` Creates a new OInstance and returns it.
`void`	`addOntologyModificationListener(OntologyModificationListener oml)` Register the Ontology Modification Listeners
`void`	`addOResourceToMap(String uri, OResource resource)` Deprecated.
`RDFProperty`	`addRDFProperty(OURI aPropertyURI, Set<OResource> domain, Set<OResource> range)` Deprecated.
`SomeValuesFromRestriction`	`addSomeValuesFromRestriction(RDFProperty onProperty, OResource hasValue)` Adds a new AllValuesFrom Restriction to the ontology.
`SymmetricProperty`	`addSymmetricProperty(OURI aPropertyURI, Set<OClass> domainAndRange)` Creates a new symmetric property (an object property that is symmetric).
`TransitiveProperty`	`addTransitiveProperty(OURI aPropertyURI, Set<OClass> domain, Set<OClass> range)` Creates a new transitive property (an object property that is transitive).
`void`	`cleanOntology()` This method removes the entire data from the ontology and emptys it.
`void`	`commitTransaction()` Deprecated.
`boolean`	`containsOClass(OClass theClass)` Checks whether the ontology contains this class.
`boolean`	`containsOClass(ONodeID theURI)` Checks whether a class with the specified URI or blank node ID exists in the ontology.
`boolean`	`containsOInstance(OInstance theInstance)` Checks whether the provided Instance exists in the ontology.
`boolean`	`containsOInstance(OURI theInstanceURI)` Checks whether the provided URI refers to an Instance that exists in the ontology.
`OntologyBooleanQuery`	`createBooleanQuery(String theQuery, OConstants.QueryLanguage queryLanguage)` This method creates a OntologyBooleanQuery object and passes on the specified query string and the specified query language.
`OURI`	`createOURI(String theURI)` Create an ORUI object from the given URI string.
`OURI`	`createOURIForName(String resourceName)` Create an OURI from the given resource name, using the ontology base URI (default name space).
`OntologyTupleQuery`	`createTupleQuery(String theQuery, OConstants.QueryLanguage queryLanguage)` This method creates a OntologyTupleQuery object and passes on the specified query string in the specified query language.
`String`	`executeQuery(String serqlQuery)` Deprecated.
`void`	`fireOntologyReset()` A method to invoke when the ontology is reset.
`void`	`fireOntologyResourceAdded(OResource resource)` A Method to invoke an event for newly added ontology resource
`void`	`fireOntologyResourcesRemoved(String[] resources)` A Method to invoke an event for a removed ontology resource
`void`	`fireResourcePropertyValueChanged(OResource resource, RDFProperty property, Object value, int eventType)` A method to invoke when a resource's property value is changed
`void`	`fireResourceRelationChanged(OResource resource1, OResource resource2, int eventType)` A method to invoke when a resource's property value is changed
`OURI`	`generateOURI(String resourceNamePrefix)` Generate a new unique OURI for this ontology.
`OURI`	`generateOURI(String resourceNamePrefix, String baseURI)` Generate a new unique OURI for this ontology.
`List<OResource>`	`getAllResources()` Deprecated.
`Set<AnnotationProperty>`	`getAnnotationProperties()` Gets the set of Annotation Properties in the ontology where for a property there exists a statement <theProperty, RDF:Type, OWL:AnnotationProperty>.
`AnnotationProperty`	`getAnnotationProperty(OURI theURI)` Returns the annotation property for the given URI or null if there is no annotation property with that URI.
`Set<DatatypeProperty>`	`getDatatypeProperties()` Gets the set of Datatype Properties in the ontology.
`DatatypeProperty`	`getDatatypeProperty(OURI theURI)` Returns the datatype property for the given URI or null if there is no datatype property with that URI.
`String`	`getDefaultNameSpace()` Gets the default name space for this ontology.
`int`	`getDistance(OClass class1, OClass class2)` Gets the taxonomic distance between 2 classes.
`Set<ObjectProperty>`	`getObjectProperties()` Gets the set of Object Properties in the ontology.
`ObjectProperty`	`getObjectProperty(OURI theURI)` Returns the object property for the given URI or null if there is no object property with that URI.
`OClass`	`getOClass(ONodeID theClassID)` Retrieves a both named classes and anonymous classes and retrictions that match either the URI or the blank node identifier represented by ONodeID
`Set<OClass>`	`getOClasses(boolean top)` Retrieves all ontology classes in a set.
`ClosableIterator<OClass>`	`getOClassesIterator(boolean top)` Return an iterator to retrieve all ontology classes in the ontology.
`OInstance`	`getOInstance(OURI theInstanceURI)` Gets the instance with the given URI.
`Set<OInstance>`	`getOInstances()` Gets all instances in the ontology.
`Set<OInstance>`	`getOInstances(OClass theClass, byte closure)` Deprecated.
`Set<OInstance>`	`getOInstances(OClass theClass, OConstants.Closure closure)` Gets instances in the ontology, which belong to this class.
`ClosableIterator<OInstance>`	`getOInstancesIterator()`
`ClosableIterator<OInstance>`	`getOInstancesIterator(OClass theClass, OConstants.Closure closure)`
`List<Literal>`	`getOntologyAnnotationValues(AnnotationProperty ann)` Get the values of an ontology annotation property.
`String`	`getOntologyData(byte format)` Deprecated. not supported any more - throws UnsupportedOperationException
`OntologyTripleStore`	`getOntologyTripleStore()` Return an object representing the triple store which backs the ontology.
`OURI`	`getOntologyURI()` Get the URI of this ontology.
`OResource`	`getOResourceByName(String resourceName)` Deprecated.
`OResource`	`getOResourceFromMap(String uri)` Deprecated.
`List<OResource>`	`getOResourcesByName(String resourceName)` This method checks in its cache to find out the OResources for the given resource name.
`List<OResource>`	`getOResourcesWith(RDFProperty aProperty, Literal aValue)` This method given a property (either an annotation or datatype), retrieves a list of resources which have the provided literal set as a value.
`List<OResource>`	`getOResourcesWith(RDFProperty aProperty, OResource aValue)` This method given a property (either object, transitive, symmetric or rdf), retrieves a list of resources which have the provided resource set as a value.
`RDFProperty`	`getProperty(OURI thePropertyURI)` Returns the property for a given URI or null if there is no property with that URI.
`Set<RDFProperty>`	`getPropertyDefinitions()` Gets the set of RDF, Object, Datatype, Symmetric and Transitive property definitions in this ontology.
`Set<RDFProperty>`	`getRDFProperties()` Gets the set of RDF Properties in the ontology where for a property there exists a statement @lt;theProperty, RDF:Type, RDF:Property>.
`Object`	`getSesameRepository()` Deprecated.
`String`	`getSesameRepositoryID()` Deprecated.
`Set<SymmetricProperty>`	`getSymmetricProperties()` Gets the set of Symmetric Properties in the ontology.
`Set<TransitiveProperty>`	`getTransitiveProperties()` Gets the set of Transitive Properties in the ontology.
`URL`	`getURL()` Gets the URL of this ontology.
`String`	`getVersion()` Deprecated. use method getOntologyAnnotationValues instead
`boolean`	`isAnnotationProperty(OURI thePropertyURI)` Checkes whether there exists a statement <thePropertyURI, RDF:Type, OWL:AnnotationProperty> in the ontology or not.
`boolean`	`isDatatypeProperty(OURI thePropertyURI)` Checkes whether the ontology contains a datatype property with the given URI.
`boolean`	`isModified()` Checks the modified flag.
`boolean`	`isObjectProperty(OURI thePropertyURI)` Checks if there exists an object property with the given URI
`boolean`	`isRDFProperty(OURI thePropertyURI)` Checkes whether there exists a statement <thePropertyURI, RDF:Type, RDF:Property> in the ontology or not.
`boolean`	`isSymmetricProperty(OURI thePropertyURI)` Checkes whether there exists a statement <thePropertyURI, RDF:Type, OWL:SymmetricProperty> in the ontology or not.
`boolean`	`isTransitiveProperty(OURI thePropertyURI)` Checkes whether there exists a statement <thePropertyURI, RDF:Type, OWL:TransitiveProperty> in the ontology or not.
`void`	`readOntologyData(InputStream in, String baseURI, OConstants.OntologyFormat format, boolean asImport)` Read ontology data from the specified stream in the specified format and load it into the ontology.
`void`	`readOntologyData(Reader in, String baseURI, OConstants.OntologyFormat format, boolean asImport)` Read ontology data from the specified reader in the specified format and load it into the ontology.
`void`	`removeOClass(OClass theClass)` Removes a class from this ontology.
`void`	`removeOInstance(OInstance theInstance)` Removes the instance from the ontology.
`void`	`removeOntologyModificationListener(OntologyModificationListener oml)` Removed the registered ontology modification listeners
`void`	`removeOResourceFromMap(String uri)` Deprecated.
`void`	`removeProperty(RDFProperty theProperty)` A method to remove the existing propertyDefinition (exclusive of Annotation Property).
`void`	`resolveImports(Map<String,String> importMappings)` Loads all imported ontologies.
`void`	`setDefaultNameSpace(String aNameSpace)` Sets the default name space/base URI for the ontology.
`void`	`setModified(boolean isModified)` Sets the modified flag.
`void`	`setOntologyAnnotation(AnnotationProperty ann, Literal value)` Set an annotation property for the ontology to the specified literal value.
`void`	`setOntologyURI(OURI theURI)` Set the ontology URI of the current ontology.
`void`	`setURL(URL aUrl)` Set the URL of this ontology.
`void`	`setVersion(String theVersion)` Deprecated. use method setOntologyAnnotation instead
`void`	`store(File newOntology)` Deprecated. not implemented any more, throws UnsupportedOperationException
`boolean`	`transationStarted()` Deprecated.
`void`	`writeOntologyData(OutputStream out, byte format)` Deprecated. not supported any more - throws UnsupportedOperationException
`void`	`writeOntologyData(OutputStream out, OConstants.OntologyFormat format, boolean includeExports)` Write the ontology data to the provided output stream in the specified serialization format.
`void`	`writeOntologyData(Writer out, byte format)` Deprecated. not supported any more and will throw and exception in the new implementation plugin
`void`	`writeOntologyData(Writer out, OConstants.OntologyFormat format, boolean includeExports)` Write the ontology data to the provided writer in the specified serialization format.

Methods inherited from interface gate.LanguageResource
getDataStore, getLRPersistenceId, getParent, setDataStore, setLRPersistenceId, setParent, sync

Methods inherited from interface gate.Resource
cleanup, getParameterValue, init, setParameterValue, setParameterValues

Methods inherited from interface gate.util.FeatureBearer
getFeatures, setFeatures

Methods inherited from interface gate.util.NameBearer
getName, setName

- Method Detail
  - cleanOntology
```
void cleanOntology()
```
    This method removes the entire data from the ontology and emptys it. This will also re-initialize the ontology to the state it would have after creation and perform the import of system data into the ontology store (OWL and RDFS assertions).
  - getOntologyData
```
@Deprecated
String getOntologyData(byte format)
```
    Deprecated. not supported any more - throws UnsupportedOperationException
    
    Retrieves the ontology data and returns a string with the serialization of the data in the specified format.
    
    Parameters:
    
    format - the format to be used for serialization
    
    Returns:
    
    a string containing the serialization of the ontology
  - writeOntologyData
```
@Deprecated
void writeOntologyData(OutputStream out,
                                   byte format)
```
    Deprecated. not supported any more - throws UnsupportedOperationException
    
    Exports the ontology data into the provided format to the provided output stream.
    
    Parameters:
    
    out - OutputStream the serialized ontology data is written to
    
    format - the serialization format, see OConstants
  - writeOntologyData
```
void writeOntologyData(OutputStream out,
                       OConstants.OntologyFormat format,
                       boolean includeExports)
```
    Write the ontology data to the provided output stream in the specified serialization format. The output stream has to be closed by the caller.
    
    Parameters:
    
    out - an open OutpuStream for writing the data.
    
    format - the serialization format
    
    includeExports - if false, do not write any data that was loaded as an ontology import.
    
    Since:
    
    5.1
  - writeOntologyData
```
@Deprecated
void writeOntologyData(Writer out,
                                   byte format)
```
    Deprecated. not supported any more and will throw and exception in the new implementation plugin
    
    Exports the ontology data into the provided format using the provided writer.
    
    Parameters:
    
    out - an open Writer for writing the data
    
    format - the ontology serialization format , see OConstants
  - writeOntologyData
```
void writeOntologyData(Writer out,
                       OConstants.OntologyFormat format,
                       boolean includeExports)
```
    Write the ontology data to the provided writer in the specified serialization format. The writer object has to be closed by the caller.
    
    Parameters:
    
    out - an open Writer for writing the data
    
    format - the ontology serialization format , see OConstants.OntologyFormat
    
    includeExports - if false, do not write any data that was loaded as and ontology import.
  - readOntologyData
```
void readOntologyData(InputStream in,
                      String baseURI,
                      OConstants.OntologyFormat format,
                      boolean asImport)
```
    Read ontology data from the specified stream in the specified format and load it into the ontology. The input stream has to be closed by the caller.
    
    Parameters:
    
    in - an InputStream object for reading the ontology data
    
    baseURI - the URI to use for resolving URI references
    
    format - the serialization format of the ontology, see OConstants.OntologyFormat
    
    asImport - if true, load the data as an ontology import which means that it will not be written as part of the user data, unless explicitly requested.
  - readOntologyData
```
void readOntologyData(Reader in,
                      String baseURI,
                      OConstants.OntologyFormat format,
                      boolean asImport)
```
    Read ontology data from the specified reader in the specified format and load it into the ontology.
    
    Parameters:
    
    in -
    
    baseURI -
    
    format -
    
    asImport - asImport if true, load the data as an ontology import which means that it will not be written as part of the user data, unless explicitly requested.
  - getOntologyURI
```
OURI getOntologyURI()
```
    Get the URI of this ontology. If no ontology URI is found, null is returned. If more than one ontology URI is found, an exception is thrown.
    
    Returns:
    
    the OURI of the current ontology or null
  - setOntologyURI
```
void setOntologyURI(OURI theURI)
```
    Set the ontology URI of the current ontology. If the ontology URI is already set to a different value, this method throws an exception.
    NOTE: this method does not set the default namespace!
    NOTE: at the moment, this method allows to set the ontology URI as long as no URI is set yet. Once an ontology URI is set, it cannot be changed since it would not be clear what to do with assertions that alreadt reference that ontology URI (e.g. ontology annotations or import specifications).
    
    Parameters:
    
    theURI -
  - resolveImports
```
void resolveImports(Map<String,String> importMappings)
```
    Loads all imported ontologies. This method finds all ontology import URIs in the current ontology and loads as imports the ontologies referenced by these URIs. If an URI is found in importMappings, and maps to an empty String, the import will be ignored. If an URI is found and maps to a non-empty string, the string will be interpreted as an URL from which to load the imported ontology. If no entry is found for the URI, the URI will be interpreted as an URL from which to load the ontology. All import URIs of ontologies loaded during this process will be recursively processed in the same way. A GateOntologyException is thrown if any import that should be loaded cannot be loaded and the import loading process is aborted before potential additional imports are processed.
    
    Parameters:
    
    importMappings -
  - getURL
```
URL getURL()
```
    Gets the URL of this ontology. This usually is the URL the ontology was loaded from. If several files were loaded, the URL of the first file is returned. Files loaded as imports are not considered for this. If and how this is set automatically when an ontology LR is created depends on the implementation. For an ontology LR that connects to an existing ontology repository, an URL derived from the ontology repository location may be returned.
    
    Returns:
    
    the URL of this ontology if set, or null otherwise
  - setURL
```
void setURL(URL aUrl)
```
    Set the URL of this ontology. This URL set by this method will be returned by the getURL() method. The ontology store is not modified by this.
    
    Parameters:
    
    aUrl - the url to be set
  - store
```
@Deprecated
void store(File newOntology)
                throws IOException
```
    Deprecated. not implemented any more, throws UnsupportedOperationException
    
    Saves the ontology in the specified File
    
    Parameters:
    
    newOntology - a File object describing the file where to save to
    
    Throws:
    
    IOException
  - setDefaultNameSpace
```
void setDefaultNameSpace(String aNameSpace)
```
    Sets the default name space/base URI for the ontology. This URI must end in "#" or "/". This URI is used when a new OURI is created using the createOURIForName(String) method. Setting the default name space with this method does not change the ontology store and does not add a default namespace declaration to the store or when the ontology is saved.
    
    Parameters:
    
    aNameSpace - a String that can be used as a base URI
  - getDefaultNameSpace
```
String getDefaultNameSpace()
```
    Gets the default name space for this ontology. This is used as the base URI for the ontology. This returns the last value set with the method setDefaultNameSpace. If the default name space was not set with this method, it is set to a default value when an ontology is loaded in the following way: If a base URI is specified for the loading, that base URI is used, otherwise, if there was no ontology URI already set from a previous load and this load determined exactly one ontology URI, that URI will be used to set the default name space.
    
    Returns:
    
    a String value.
  - setVersion
```
@Deprecated
void setVersion(String theVersion)
```
    Deprecated. use method setOntologyAnnotation instead
    
    Sets the version information for the ontology.
    
    Parameters:
    
    theVersion - the version to be set
  - getVersion
```
@Deprecated
String getVersion()
```
    Deprecated. use method getOntologyAnnotationValues instead
    
    Gets the version of this ontology.
    
    Returns:
    
    the version of this ontology
  - setOntologyAnnotation
```
void setOntologyAnnotation(AnnotationProperty ann,
                           Literal value)
```
    Set an annotation property for the ontology to the specified literal value.
    
    Parameters:
    
    ann - the annotation property object
    
    value - a Literal object describing the value. This usually should be a String literal.
  - getOntologyAnnotationValues
```
List<Literal> getOntologyAnnotationValues(AnnotationProperty ann)
```
    Get the values of an ontology annotation property.
    
    Parameters:
    
    ann - the annotation property object
    
    Returns:
    
    a a list of literals describing the values for the property
  - addOClass
```
@Deprecated
OClass addOClass(OURI aURI,
                             byte classType)
```
    Deprecated. - use one of the dedicated methods to add a named class or a restriction instead
    
    Creates a new OClass and adds it the ontology.
    
    Parameters:
    
    aURI - URI of this class
    
    classType - one of the values from OConstants.OCLASS_TYPE_OWL_CLASS and OConstants.OCLASS_TYPE_OWL_RESTRICTION;
    
    Returns:
    
    the newly created class or an existing class if available with the same URI.
  - addOClass
```
OClass addOClass(OURI aURI)
```
    Creates a new OWL Class and adds it the ontology. If a class with that URI already exists, that class is returned.
    
    Parameters:
    
    aURI - URI of this class
    
    Returns:
    
    the newly created class or an existing class if available with the same URI.
  - getOClass
```
OClass getOClass(ONodeID theClassID)
```
    Retrieves a both named classes and anonymous classes and retrictions that match either the URI or the blank node identifier represented by ONodeID
    
    Parameters:
    
    theClassID -
    
    Returns:
    
    the class matching the URI or blank node ID or null if no matches.
  - removeOClass
```
void removeOClass(OClass theClass)
```
    Removes a class from this ontology.
    
    Parameters:
    
    theClass - the class to be removed
  - containsOClass
```
boolean containsOClass(ONodeID theURI)
```
    Checks whether a class with the specified URI or blank node ID exists in the ontology.
    
    Parameters:
    
    theURI - a ONodeID, usually an OURI specifying the ID of the ontology class
    
    Returns:
    
    true, if the class exists
  - containsOClass
```
boolean containsOClass(OClass theClass)
```
    Checks whether the ontology contains this class.
    
    Parameters:
    
    theClass - a ontology class object
    
    Returns:
    
    true, if the class exists, otherwise - false.
  - getOClasses
```
Set<OClass> getOClasses(boolean top)
```
    Retrieves all ontology classes in a set. This method returns a set of either all classes in the ontology or just the "top" classes. A "top" class is a class that is not a subclass of any other class that is not a predefined system class like owl:Thing or rdfs:Resource or a trivial subclass (of itself or of a class that is defined to be equivalent to itself).
    NOTE: for large ontologies with a large number of classes it may be preferable to use method getOClassesIterator(boolean) instead.
    
    Parameters:
    
    top - If set to true, only returns those classes with no super classes, otherwise - a set of all classes.
    
    Returns:
    
    set of all the classes in this ontology
  - getOClassesIterator
```
ClosableIterator<OClass> getOClassesIterator(boolean top)
```
    Return an iterator to retrieve all ontology classes in the ontology. The iterator should be closed() as soon as it is not needed anymore but will auto-close when it is exhausted and the hasNext() method returned false.
    
    Parameters:
    
    top - If set to true, only returns those classes with no super classes, otherwise all classes
    
    Returns:
    
    a ClosableIterator for accessing the returned ontology classes
  - getDistance
```
int getDistance(OClass class1,
                OClass class2)
```
    Gets the taxonomic distance between 2 classes.
    
    Parameters:
    
    class1 - the first class
    
    class2 - the second class
    
    Returns:
    
    the taxonomic distance between the 2 classes
  - addOInstance
```
OInstance addOInstance(OURI theInstanceURI,
                       OClass theClass)
```
    Creates a new OInstance and returns it.
    
    Parameters:
    
    theInstanceURI -
    
    theClass - the class to which the instance belongs.
    
    Returns:
    
    the OInstance that has been added to the ontology.
  - removeOInstance
```
void removeOInstance(OInstance theInstance)
```
    Removes the instance from the ontology.
    
    Parameters:
    
    theInstance - to be removed
  - getOInstances
```
Set<OInstance> getOInstances()
```
    Gets all instances in the ontology.
    
    Returns:
    
    a Set of OInstance objects
  - getOInstancesIterator
```
ClosableIterator<OInstance> getOInstancesIterator()
```
  - getOInstances
```
@Deprecated
Set<OInstance> getOInstances(OClass theClass,
                                         byte closure)
```
    Deprecated.
    
    Gets instances in the ontology, which belong to this class.
    
    Parameters:
    
    theClass - the class of the instances
    
    closure - either DIRECT_CLOSURE or TRANSITIVE_CLOSURE of OConstants
    
    Returns:
    
    Set of OInstance objects
  - getOInstances
```
Set<OInstance> getOInstances(OClass theClass,
                             OConstants.Closure closure)
```
    Gets instances in the ontology, which belong to this class. The second parameter specifies if the the given class needs to be a direct class of the instance (direct closure) or a class to which the instance belongs indirectly (transitive closure)
    
    Parameters:
    
    theClass - the class of the instances
    
    closure - either OConstants.Closure.DIRECT_CLOSURE or OConstants.Closure.TRANSITIVE_CLOSURE
    
    Returns:
    
    Set of OInstance objects
  - getOInstancesIterator
```
ClosableIterator<OInstance> getOInstancesIterator(OClass theClass,
                                                  OConstants.Closure closure)
```
  - getOInstance
```
OInstance getOInstance(OURI theInstanceURI)
```
    Gets the instance with the given URI.
    
    Parameters:
    
    theInstanceURI - the instance URI
    
    Returns:
    
    the OInstance object with this URI. If there is no such instance then null.
  - containsOInstance
```
boolean containsOInstance(OInstance theInstance)
```
    Checks whether the provided Instance exists in the ontology.
    
    Parameters:
    
    theInstance -
    
    Returns:
    
    true, if the Instance exists in ontology, otherwise - false.
  - containsOInstance
```
boolean containsOInstance(OURI theInstanceURI)
```
    Checks whether the provided URI refers to an Instance that exists in the ontology.
    
    Parameters:
    
    theInstanceURI -
    
    Returns:
    
    true, if the URI exists in ontology and refers to an Instance, otherwise - false.
  - addRDFProperty
```
@Deprecated
RDFProperty addRDFProperty(OURI aPropertyURI,
                                       Set<OResource> domain,
                                       Set<OResource> range)
```
    Deprecated.
    
    Creates a new RDFProperty.
    
    Parameters:
    
    aPropertyURI - URI of the property to be added into the ontology.
    
    domain - a set of OResource (e.g. a Class, a Property etc.).
    
    range - a set of OResource (e.g. a Class, a Property etc.).
  - getRDFProperties
```
Set<RDFProperty> getRDFProperties()
```
    Gets the set of RDF Properties in the ontology where for a property there exists a statement @lt;theProperty, RDF:Type, RDF:Property>.
    
    Returns:
    
    a Set of RDFProperty.
  - isRDFProperty
```
boolean isRDFProperty(OURI thePropertyURI)
```
    Checkes whether there exists a statement <thePropertyURI, RDF:Type, RDF:Property> in the ontology or not.
    
    Parameters:
    
    thePropertyURI -
    
    Returns:
    
    true, only if there exists the above statement, otherwise - false.
  - addAnnotationProperty
```
AnnotationProperty addAnnotationProperty(OURI aPropertyURI)
```
    Creates a new AnnotationProperty.
    
    Parameters:
    
    aPropertyURI - URI of the property to be added into the ontology.
  - getAnnotationProperties
```
Set<AnnotationProperty> getAnnotationProperties()
```
    Gets the set of Annotation Properties in the ontology where for a property there exists a statement <theProperty, RDF:Type, OWL:AnnotationProperty>.
    
    Returns:
    
    a Set of AnnotationProperty.
  - isAnnotationProperty
```
boolean isAnnotationProperty(OURI thePropertyURI)
```
    Checkes whether there exists a statement <thePropertyURI, RDF:Type, OWL:AnnotationProperty> in the ontology or not.
    
    Parameters:
    
    thePropertyURI -
    
    Returns:
    
    true, only if there exists the above statement, otherwise - false.
  - addDatatypeProperty
```
DatatypeProperty addDatatypeProperty(OURI aPropertyURI,
                                     Set<OClass> domain,
                                     DataType aDatatype)
```
    Create a DatatypeProperty with the given domain and range. The domain must be specified as a set of OClass objects, the resulting domain is the intersection of all specified classes.
    If this method is called with an OURI of a datatype property that already exists, any specified domain class is added to the intersection of classes already defined for the domain.
    
    Parameters:
    
    aPropertyURI - the URI for the new property.
    
    domain - the set of ontology classes that constitutes the domain for the new property.
    
    aDatatype - a DataType object describing the datatype of the range.
    
    Returns:
    
    the newly created property.
  - getDatatypeProperties
```
Set<DatatypeProperty> getDatatypeProperties()
```
    Gets the set of Datatype Properties in the ontology.
    
    Returns:
    
    a Set of DatatypeProperty.
  - isDatatypeProperty
```
boolean isDatatypeProperty(OURI thePropertyURI)
```
    Checkes whether the ontology contains a datatype property with the given URI.
    
    Parameters:
    
    thePropertyURI -
    
    Returns:
    
    true if there is an instance of owl:DatatypeProperty with the given URI in the ontology.
  - addObjectProperty
```
ObjectProperty addObjectProperty(OURI aPropertyURI,
                                 Set<OClass> domain,
                                 Set<OClass> range)
```
    Creates a new object property (a property that takes instances as values).
    If this method is called with an OURI of an object property that already exists, any specified domain or range class is added to the intersection of classes already defined for the domain or range.
    
    Parameters:
    
    aPropertyURI - the URI for the new property.
    
    domain - the set of ontology classes (i.e. OClass objects} that constitutes the domain of the property. An instance must belong to the intersection of all classes in the set to be a valid member of the domain of the property. If an empty set or null is passed, the instance can belong to any class.
    
    range - the set of ontology classes (i.e. OClass objects} that constitutes the range for the new property. The instance that is the value of a property must belong to the intersection of all classes in this set to be valid. If an empty set or null is passed on, the instance can belong to any class.
    
    Returns:
    
    the newly created property.
  - getObjectProperties
```
Set<ObjectProperty> getObjectProperties()
```
    Gets the set of Object Properties in the ontology.
    
    Returns:
    
    a Set of ObjectProperty.
  - isObjectProperty
```
boolean isObjectProperty(OURI thePropertyURI)
```
    Checks if there exists an object property with the given URI
    
    Parameters:
    
    thePropertyURI -
    
    Returns:
    
    true, only if there exists an object property with the given URI.
  - addSymmetricProperty
```
SymmetricProperty addSymmetricProperty(OURI aPropertyURI,
                                       Set<OClass> domainAndRange)
```
    Creates a new symmetric property (an object property that is symmetric).
    If this method is called with an OURI of a datatype property that already exists, any specified domainAndRange class is added to the intersection of classes already defined for the domain and range.
    
    Parameters:
    
    aPropertyURI - the URI for the new property.
    
    domainAndRange - the set of ontology classes (i.e. OClass objects} that constitutes the domain and the range for the new property. The property only applies to instances that belong to the intersection of all classes included in its domain. An empty set means that the property applies to instances of any class.
    
    Returns:
    
    the newly created property.
  - getSymmetricProperties
```
Set<SymmetricProperty> getSymmetricProperties()
```
    Gets the set of Symmetric Properties in the ontology.
    
    Returns:
    
    a Set of SymmetricProperty.
  - isSymmetricProperty
```
boolean isSymmetricProperty(OURI thePropertyURI)
```
    Checkes whether there exists a statement <thePropertyURI, RDF:Type, OWL:SymmetricProperty> in the ontology or not.
    
    Parameters:
    
    thePropertyURI -
    
    Returns:
    
    true, only if there exists the above statement, otherwise - false.
  - addTransitiveProperty
```
TransitiveProperty addTransitiveProperty(OURI aPropertyURI,
                                         Set<OClass> domain,
                                         Set<OClass> range)
```
    Creates a new transitive property (an object property that is transitive). If this method is called with an OURI of a transitive property that already exists, any specified domain or range class is added to the intersection of classes already defined for the domain or range.
    
    Parameters:
    
    aPropertyURI - the URI for the new property.
    
    domain - the set of ontology classes (i.e. OClass objects} that constitutes the range for the new property. The property only applies to instances that belong to the intersection of all classes included in its domain. An empty set means that the property applies to instances of any class.
    
    range - the set of ontology classes (i.e. OClass objects} that constitutes the range for the new property.
    
    Returns:
    
    the newly created property.
  - getTransitiveProperties
```
Set<TransitiveProperty> getTransitiveProperties()
```
    Gets the set of Transitive Properties in the ontology.
    
    Returns:
    
    a Set of TransitiveProperty.
  - isTransitiveProperty
```
boolean isTransitiveProperty(OURI thePropertyURI)
```
    Checkes whether there exists a statement <thePropertyURI, RDF:Type, OWL:TransitiveProperty> in the ontology or not.
    
    Parameters:
    
    thePropertyURI -
    
    Returns:
    
    true, only if there exists the above statement, otherwise - false.
  - getPropertyDefinitions
```
Set<RDFProperty> getPropertyDefinitions()
```
    Gets the set of RDF, Object, Datatype, Symmetric and Transitive property definitions in this ontology.
    
    Returns:
    
    a Set of RDFProperty, DatatypeProperty, ObjectProperty, TransitiveProperty and , SymmetricProperty objects. Please note that the method does not include annotation properties.
  - getProperty
```
RDFProperty getProperty(OURI thePropertyURI)
```
    Returns the property for a given URI or null if there is no property with that URI.
    
    Parameters:
    
    thePropertyURI - the URI of the property
    
    Returns:
    
    the RDFProperty object or null if no property with that URI is found
  - getAnnotationProperty
```
AnnotationProperty getAnnotationProperty(OURI theURI)
```
    Returns the annotation property for the given URI or null if there is no annotation property with that URI.
    
    Parameters:
    
    theURI - the URI of the property
    
    Returns:
    
    the AnnotationProperty obejct
  - getDatatypeProperty
```
DatatypeProperty getDatatypeProperty(OURI theURI)
```
    Returns the datatype property for the given URI or null if there is no datatype property with that URI.
    
    Parameters:
    
    theURI - the URI of the property
    
    Returns:
    
    the DatatypeProperty obejct
  - getObjectProperty
```
ObjectProperty getObjectProperty(OURI theURI)
```
    Returns the object property for the given URI or null if there is no object property with that URI.
    
    Parameters:
    
    theURI - the URI of the property
    
    Returns:
    
    the AnnotationProperty obejct
  - removeProperty
```
void removeProperty(RDFProperty theProperty)
```
    A method to remove the existing propertyDefinition (exclusive of Annotation Property).
    
    Parameters:
    
    theProperty -
  - addMinCardinalityRestriction
```
MinCardinalityRestriction addMinCardinalityRestriction(RDFProperty onProperty,
                                                       String minCardinalityValue)
                                                throws InvalidValueException
```
    Adds a new MinCardinality Restriction to the ontology. It automatically creates a randon anonymous class, which it uses to denote the restriction. The default datatype is set to NonNegativeIntegerNumber
    
    Parameters:
    
    onProperty - - Specifies the property for which the restriction is being set.
    
    minCardinalityValue - - generally a numeric number.
    
    Throws:
    
    InvalidValueException - - if a value is not compatible with the nonNegativeIntegerNumber datatype.
  - addMaxCardinalityRestriction
```
MaxCardinalityRestriction addMaxCardinalityRestriction(RDFProperty onProperty,
                                                       String maxCardinalityValue)
                                                throws InvalidValueException
```
    Adds a new MaxCardinality Restriction to the ontology. It automatically creates a randon anonymous class, which it uses to denote the restriction. The default datatype is set to NonNegativeIntegerNumber
    
    Parameters:
    
    onProperty - - Specifies the property for which the restriction is being set.
    
    maxCardinalityValue - - generally a numeric number.
    
    Throws:
    
    InvalidValueException - - if a value is not compatible with the nonNegativeIntegerNumber datatype.
  - addCardinalityRestriction
```
CardinalityRestriction addCardinalityRestriction(RDFProperty onProperty,
                                                 String cardinalityValue)
                                          throws InvalidValueException
```
    Adds a new Cardinality Restriction to the ontology. It automatically creates a randon anonymous class, which it uses to denote the restriction. The default datatype is set to NonNegativeIntegerNumber
    
    Parameters:
    
    onProperty - - Specifies the property for which the restriction is being set.
    
    cardinalityValue - - generally a numeric number.
    
    Throws:
    
    InvalidValueException - - if a value is not compatible with the nonNegativeIntegerNumber datatype.
  - addHasValueRestriction
```
HasValueRestriction addHasValueRestriction(RDFProperty onProperty,
                                           OResource hasValue)
```
    Adds a new HasValue Restriction to the ontology. It automatically creates a randon anonymous class, which it uses to denote the restriction.
    
    Parameters:
    
    onProperty - - Specifies the property for which the restriction is being set.
    
    hasValue - - a resource used as a value for hasValue element of the restriction.
  - addAllValuesFromRestriction
```
@Deprecated
AllValuesFromRestriction addAllValuesFromRestriction(RDFProperty onProperty,
                                                                 OResource hasValue)
```
    Deprecated. - this method is deprecated and kept for backwards compatibility as long as the OntologyOWLIM2 plugin is kept. Use the method addAllValuesFromRestriction(ObjectProperty, OClass) instead.
    
    Adds a new AllValuesFrom Restriction to the ontology.
    
    Parameters:
    
    onProperty - - Specifies the property for which the restriction is being set.
    
    hasValue - - a resource used as a value for hasValue element of the restriction.
  - addAllValuesFromRestriction
```
AllValuesFromRestriction addAllValuesFromRestriction(ObjectProperty onProperty,
                                                     OClass theClass)
```
  - addSomeValuesFromRestriction
```
SomeValuesFromRestriction addSomeValuesFromRestriction(RDFProperty onProperty,
                                                       OResource hasValue)
```
    Adds a new AllValuesFrom Restriction to the ontology. It automatically creates a randon anonymous class, which it uses to denote the restriction.
    
    Parameters:
    
    onProperty - - Specifies the property for which the restriction is being set.
    
    hasValue - - a resource used as a value for hasValue element of the restriction.
  - addAnonymousClass
```
AnonymousClass addAnonymousClass()
```
  - setModified
```
void setModified(boolean isModified)
```
    Sets the modified flag.
    
    Parameters:
    
    isModified - sets this param as a value of the modified property of the ontology
  - isModified
```
boolean isModified()
```
    Checks the modified flag.
    
    Specified by:
    
    isModified in interface LanguageResource
    
    Returns:
    
    whether the ontology has been modified after the loading
  - addOntologyModificationListener
```
void addOntologyModificationListener(OntologyModificationListener oml)
```
    Register the Ontology Modification Listeners
  - removeOntologyModificationListener
```
void removeOntologyModificationListener(OntologyModificationListener oml)
```
    Removed the registered ontology modification listeners
  - fireResourcePropertyValueChanged
```
void fireResourcePropertyValueChanged(OResource resource,
                                      RDFProperty property,
                                      Object value,
                                      int eventType)
```
    A method to invoke when a resource's property value is changed
  - fireResourceRelationChanged
```
void fireResourceRelationChanged(OResource resource1,
                                 OResource resource2,
                                 int eventType)
```
    A method to invoke when a resource's property value is changed
    
    Parameters:
    
    resource1 -
    
    resource2 -
    
    eventType -
  - fireOntologyResourceAdded
```
void fireOntologyResourceAdded(OResource resource)
```
    A Method to invoke an event for newly added ontology resource
    
    Parameters:
    
    resource -
  - fireOntologyResourcesRemoved
```
void fireOntologyResourcesRemoved(String[] resources)
```
    A Method to invoke an event for a removed ontology resource
    
    Parameters:
    
    resources -
  - fireOntologyReset
```
void fireOntologyReset()
```
    A method to invoke when the ontology is reset.
  - commitTransaction
```
@Deprecated
void commitTransaction()
```
    Deprecated.
    
    Commit all changes to the ontology. This will commit all changesall the transaction (so far included after the call to start transaction) into the repository.
  - transationStarted
```
@Deprecated
boolean transationStarted()
```
    Deprecated.
    
    Checks whether the transation is already started.
  - getSesameRepository
```
@Deprecated
Object getSesameRepository()
```
    Deprecated.
    
    Returns the repository created for this particular instance of the ontology.
  - getSesameRepositoryID
```
@Deprecated
String getSesameRepositoryID()
```
    Deprecated.
    
    Returns the ID of a Sesame Repository created for this particular instance of the ontology.
  - getOResourceFromMap
```
@Deprecated
OResource getOResourceFromMap(String uri)
```
    Deprecated.
    
    Given a URI object, this method returns its equivalent object
  - addOResourceToMap
```
@Deprecated
void addOResourceToMap(String uri,
                                   OResource resource)
```
    Deprecated.
    
    Adds the resource to central map
  - removeOResourceFromMap
```
@Deprecated
void removeOResourceFromMap(String uri)
```
    Deprecated.
    
    Removes the resource from the central map
    
    Parameters:
    
    uri -
  - getOResourceByName
```
@Deprecated
OResource getOResourceByName(String resourceName)
```
    Deprecated.
    
    This method checks in its cache to find out the OResource for the given resource name. However, It is also possible for two resources to have a same name but different name spaces. This method returns the first found OResource (without guaranteeing the order) from its list. If user wants to retrieve a list of resources, he/she must use the getOResourcesByName(String resourceName).
  - getOResourcesByName
```
List<OResource> getOResourcesByName(String resourceName)
```
    This method checks in its cache to find out the OResources for the given resource name. It is possible for two resources to have a same name but different name spaces. This method returns a list of resources with the common name. Please note that deleting an instance from this list (e.g. list.remove(int/Object)) does not delete the resource from an ontology. One must use appropriate method from the Ontology interface to delete such resources.
  - getAllResources
```
@Deprecated
List<OResource> getAllResources()
```
    Deprecated.
    
    This method returns a list of OResources from the ontology. Please note that deleting an instance from this list (e.g. list.remove(int/Object)) does not delete the resource from an ontology. One must use appropriate method from the Ontology interface to delete such resources.
  - getOResourcesWith
```
List<OResource> getOResourcesWith(RDFProperty aProperty,
                                  Literal aValue)
```
    This method given a property (either an annotation or datatype), retrieves a list of resources which have the provided literal set as a value.
  - getOResourcesWith
```
List<OResource> getOResourcesWith(RDFProperty aProperty,
                                  OResource aValue)
```
    This method given a property (either object, transitive, symmetric or rdf), retrieves a list of resources which have the provided resource set as a value.
  - executeQuery
```
@Deprecated
String executeQuery(String serqlQuery)
```
    Deprecated.
    
    The method executes the query on repository and returns the toString() result of the QueryResultTable.
  - createTupleQuery
```
OntologyTupleQuery createTupleQuery(String theQuery,
                                    OConstants.QueryLanguage queryLanguage)
```
    This method creates a OntologyTupleQuery object and passes on the specified query string in the specified query language.
    
    Parameters:
    
    theQuery - a String representing the tuple query.
    
    queryLanguage - the query language, either SERQL or SPARQL
    
    Returns:
    
    the OntologyTurpleQuery object that can be used to retrieve the matching tuples in several formats. The query object can be re-used with different variable bindings.
  - createBooleanQuery
```
OntologyBooleanQuery createBooleanQuery(String theQuery,
                                        OConstants.QueryLanguage queryLanguage)
```
    This method creates a OntologyBooleanQuery object and passes on the specified query string and the specified query language.
    
    Parameters:
    
    theQuery - a String representing the tuple query.
    
    queryLanguage - the query language, either SERQL or SPARQL
    
    Returns:
    
    the OntologyBooleanQuery object that can be used to retrieve the boolean answer for the query. The query object can be re-used with different variable bindings.
  - getOntologyTripleStore
```
OntologyTripleStore getOntologyTripleStore()
```
    Return an object representing the triple store which backs the ontology.
    
    Returns:
    
    The OntologyTripleStore object for this ontology or null if modifying the ontology via triples is not supported by the implementation.
  - createOURI
```
OURI createOURI(String theURI)
```
    Create an ORUI object from the given URI string.
    
    Parameters:
    
    theURI - an URI or IRI string
    
    Returns:
    
    the OURI object representing the URI/IRI
  - createOURIForName
```
OURI createOURIForName(String resourceName)
```
    Create an OURI from the given resource name, using the ontology base URI (default name space). This method will throw an exception if no default name space is set (i.e. if the method getDefaultNameSpace would return null).
    
    Parameters:
    
    resourceName - the resource name i.e. the part of the final URI/IRI that is attached to the base URI (aftaer a trailing "#" or "/").
    
    Returns:
    
    the OURI
  - generateOURI
```
OURI generateOURI(String resourceNamePrefix)
```
    Generate a new unique OURI for this ontology. This generates a new OURI that is guaranteed to be unique in the ontology, using the specified resource name string as a prefix for the URI's fragement identifier and the current defaultNameSpace of the ontology as a base URI. The resource name can be null or the empty string if no prefix is wanted.
    The URI fragment part that is appended to the given resourceName (if any) consists of 7 ASCII characters representing the system time in radix 36 followed by 3 ASCII characters representing a random number.
    Note that this method will return an OURI that is guaranteed not to be contained in the ontology, but if called repeatedly without actually adding a resource with the newly generated OURI to the ontology, the method might, although extremely unlikely, still return the same OURI more than once. Generated OURIs should hence been used for adding resources before more OURIs are generated.
    
    Parameters:
    
    resourceNamePrefix - the prefix to use for the generated resource name
    
    Returns:
    
    a OURI object for an URI that is new and unique in the ontology
  - generateOURI
```
OURI generateOURI(String resourceNamePrefix,
                  String baseURI)
```
    Generate a new unique OURI for this ontology. This works in the same way as generateOURI(java.lang.String) but also allows the specification of the base URI part of the final URI.
    
    Parameters:
    
    resourceNamePrefix - the prefix to use for the generated resource name
    
    baseURI - the base URI to use for the final URI
    
    Returns:
    
    a OURI object for an URI that is new and unique in the ontology

Interface Ontology

Method Summary

Methods inherited from interface gate.LanguageResource

Methods inherited from interface gate.Resource

Methods inherited from interface gate.util.FeatureBearer

Methods inherited from interface gate.util.NameBearer

Method Detail

cleanOntology

getOntologyData

writeOntologyData

writeOntologyData

writeOntologyData

writeOntologyData

readOntologyData

readOntologyData

getOntologyURI

setOntologyURI

resolveImports

getURL

setURL

store

setDefaultNameSpace

getDefaultNameSpace

setVersion

getVersion

setOntologyAnnotation

getOntologyAnnotationValues

addOClass

addOClass

getOClass

removeOClass

containsOClass

containsOClass

getOClasses

getOClassesIterator

getDistance

addOInstance

removeOInstance

getOInstances

getOInstancesIterator

getOInstances

getOInstances

getOInstancesIterator

getOInstance

containsOInstance

containsOInstance

addRDFProperty

getRDFProperties

isRDFProperty

addAnnotationProperty

getAnnotationProperties

isAnnotationProperty

addDatatypeProperty

getDatatypeProperties

isDatatypeProperty

addObjectProperty

getObjectProperties

isObjectProperty

addSymmetricProperty

getSymmetricProperties

isSymmetricProperty

addTransitiveProperty

getTransitiveProperties

isTransitiveProperty

getPropertyDefinitions

getProperty

getAnnotationProperty

getDatatypeProperty

getObjectProperty

removeProperty

addMinCardinalityRestriction

addMaxCardinalityRestriction

addCardinalityRestriction

addHasValueRestriction

addAllValuesFromRestriction

addAllValuesFromRestriction

addSomeValuesFromRestriction

addAnonymousClass

setModified

isModified