org.molgenis.ontology.utils

Class OntologyLoader

java.lang.Object

org.molgenis.ontology.utils.OntologyLoader

public class OntologyLoader
extends Object

Constructor Summary

Constructors

Constructor and Description
OntologyLoader(org.semanticweb.owlapi.model.OWLOntologyManager manager, org.semanticweb.owlapi.model.OWLDataFactory factory)
OntologyLoader(String ontologyName, File ontologyFile)

Method Summary

Modifier and Type	Method and Description
void	addClass(org.semanticweb.owlapi.model.OWLClass cls, org.semanticweb.owlapi.model.OWLClass parentClass)
void	addSynonymsProperties(Set<String> synonymsProperties)
long	count()
org.semanticweb.owlapi.model.OWLClass	createClass(String iri, Set<org.semanticweb.owlapi.model.OWLClass> rootClasses)
String	extractOWLClassId(org.semanticweb.owlapi.model.OWLEntity cls)
Set<org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom>	getAllAnnotationAxiom(org.semanticweb.owlapi.model.OWLClass cls)
Set<org.semanticweb.owlapi.model.OWLClass>	getAllclasses()
Map<String,Set<String>>	getAllDatabaseIds(org.semanticweb.owlapi.model.OWLClass entity)
List<Set<org.semanticweb.owlapi.model.OWLClass>>	getAssociatedClasses(org.semanticweb.owlapi.model.OWLClass cls)
Set<org.semanticweb.owlapi.model.OWLClass>	getChildClass(org.semanticweb.owlapi.model.OWLClass cls)
Set<String>	getDatabaseIds(org.semanticweb.owlapi.model.OWLClass entity)
String	getDefinition(org.semanticweb.owlapi.model.OWLClass cls)
Map<String,org.semanticweb.owlapi.model.OWLClass>	getHashToRetrieveClass()
String	getId(org.semanticweb.owlapi.model.OWLClass entity)
String	getLabel(org.semanticweb.owlapi.model.OWLEntity entity)
String	getOntologyFilePath()
String	getOntologyIRI()
String	getOntologyLabel()
String	getOntologyName()
Set<org.semanticweb.owlapi.model.OWLClass>	getRootClasses()
Set<org.semanticweb.owlapi.model.OWLSubClassOfAxiom>	getSubClassAxiomsForSubClass(org.semanticweb.owlapi.model.OWLClass cls)
Set<org.semanticweb.owlapi.model.OWLSubClassOfAxiom>	getSubClassAxiomsForSuperClass(org.semanticweb.owlapi.model.OWLClass cls)
Set<String>	getSynonyms(org.semanticweb.owlapi.model.OWLClass cls)
org.semanticweb.owlapi.model.OWLClass	getTopClass()
void	loadOntology(String ontologyName, File ontologyFile)
void	preProcessing()

Methods inherited from class java.lang.Object

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

Constructor Detail

OntologyLoader

public OntologyLoader(org.semanticweb.owlapi.model.OWLOntologyManager manager,
                      org.semanticweb.owlapi.model.OWLDataFactory factory)

OntologyLoader

public OntologyLoader(String ontologyName,
                      File ontologyFile)
               throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException

Method Detail

loadOntology

public void loadOntology(String ontologyName,
                         File ontologyFile)
                  throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException

preProcessing

public void preProcessing()

getAllAnnotationAxiom

public Set<org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom> getAllAnnotationAxiom(org.semanticweb.owlapi.model.OWLClass cls)

getRootClasses

public Set<org.semanticweb.owlapi.model.OWLClass> getRootClasses()

getTopClass

public org.semanticweb.owlapi.model.OWLClass getTopClass()

getAssociatedClasses

public List<Set<org.semanticweb.owlapi.model.OWLClass>> getAssociatedClasses(org.semanticweb.owlapi.model.OWLClass cls)

getChildClass

public Set<org.semanticweb.owlapi.model.OWLClass> getChildClass(org.semanticweb.owlapi.model.OWLClass cls)

getId

public String getId(org.semanticweb.owlapi.model.OWLClass entity)

getSynonyms

public Set<String> getSynonyms(org.semanticweb.owlapi.model.OWLClass cls)

getDefinition

public String getDefinition(org.semanticweb.owlapi.model.OWLClass cls)

getLabel

public String getLabel(org.semanticweb.owlapi.model.OWLEntity entity)

getAllDatabaseIds

public Map<String,Set<String>> getAllDatabaseIds(org.semanticweb.owlapi.model.OWLClass entity)

getDatabaseIds

public Set<String> getDatabaseIds(org.semanticweb.owlapi.model.OWLClass entity)

getOntologyLabel

public String getOntologyLabel()

extractOWLClassId

public String extractOWLClassId(org.semanticweb.owlapi.model.OWLEntity cls)

getOntologyIRI

public String getOntologyIRI()

getOntologyName

public String getOntologyName()

getOntologyFilePath

public String getOntologyFilePath()

getHashToRetrieveClass

public Map<String,org.semanticweb.owlapi.model.OWLClass> getHashToRetrieveClass()

getSubClassAxiomsForSuperClass

public Set<org.semanticweb.owlapi.model.OWLSubClassOfAxiom> getSubClassAxiomsForSuperClass(org.semanticweb.owlapi.model.OWLClass cls)

getSubClassAxiomsForSubClass

public Set<org.semanticweb.owlapi.model.OWLSubClassOfAxiom> getSubClassAxiomsForSubClass(org.semanticweb.owlapi.model.OWLClass cls)

addSynonymsProperties

public void addSynonymsProperties(Set<String> synonymsProperties)

createClass

public org.semanticweb.owlapi.model.OWLClass createClass(String iri,
                                                         Set<org.semanticweb.owlapi.model.OWLClass> rootClasses)

addClass

public void addClass(org.semanticweb.owlapi.model.OWLClass cls,
                     org.semanticweb.owlapi.model.OWLClass parentClass)

count

public long count()

getAllclasses

public Set<org.semanticweb.owlapi.model.OWLClass> getAllclasses()