owltools.mooncat
Class PropertyViewOntologyBuilder

java.lang.Object
  extended by owltools.mooncat.PropertyViewOntologyBuilder

public class PropertyViewOntologyBuilder
extends Object


Constructor Summary
PropertyViewOntologyBuilder(org.semanticweb.owlapi.model.OWLDataFactory owlDataFactory, org.semanticweb.owlapi.model.OWLOntologyManager owlOntologyManager, org.semanticweb.owlapi.model.OWLOntology sourceOntology, org.semanticweb.owlapi.model.OWLOntology unitsOntology, org.semanticweb.owlapi.model.OWLObjectProperty viewProperty)
           
PropertyViewOntologyBuilder(org.semanticweb.owlapi.model.OWLOntology sourceOntology, org.semanticweb.owlapi.model.OWLOntology unitsOntology, org.semanticweb.owlapi.model.OWLObjectProperty viewProperty)
           
 
Method Summary
 void addViewEntities(Set<org.semanticweb.owlapi.model.OWLEntity> newEntities)
           
 void buildInferredViewOntology(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
          Once the PVO has been constructed, this uses a reasoner to classify it.
 void buildViewOntology()
           
 void buildViewOntology(org.semanticweb.owlapi.model.IRI avoIRI, org.semanticweb.owlapi.model.IRI ivoIRI)
          Constructs view ontology (PVO) from source ontology (SO), such that every class C in SO has a corresponding view class C', such that C' == P some C The PVO imports both the SO, and the elements ontology Also prepares the inferred view ontology (IPVO) You must call buildInferredViewOntology yourself (because you need to set up the reasoner object yourself)
 org.semanticweb.owlapi.model.OWLOntology getAssertedViewOntology()
          Automatically generated Property View Ontology, containing axioms C' == P some C, for each C in source ontology
 org.semanticweb.owlapi.model.OWLOntology getInferredViewOntology()
          Generated after running buildInferredViewOntology.
 Set<org.semanticweb.owlapi.model.OWLEntity> getViewEntities()
          The set of all entities in the view ontology
 String getViewLabelPrefix()
           
 String getViewLabelSuffix()
           
 org.semanticweb.owlapi.model.OWLClass getViewRootClass()
          typically [P some owl:Thing]
 void setAssertedViewOntology(org.semanticweb.owlapi.model.OWLOntology assertedViewOntology)
           
 void setInferredViewOntology(org.semanticweb.owlapi.model.OWLOntology inferredViewOntology)
           
 void setViewEntities(Set<org.semanticweb.owlapi.model.OWLEntity> viewEntities)
           
 void setViewLabelPrefix(String viewLabelPrefix)
           
 void setViewLabelPrefixAndSuffix(String viewLabelPrefix, String viewLabelSuffix)
           
 void setViewLabelSuffix(String viewLabelSuffix)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PropertyViewOntologyBuilder

public PropertyViewOntologyBuilder(org.semanticweb.owlapi.model.OWLOntology sourceOntology,
                                   org.semanticweb.owlapi.model.OWLOntology unitsOntology,
                                   org.semanticweb.owlapi.model.OWLObjectProperty viewProperty)
Parameters:
sourceOntology -
unitsOntology -
viewProperty -

PropertyViewOntologyBuilder

public PropertyViewOntologyBuilder(org.semanticweb.owlapi.model.OWLDataFactory owlDataFactory,
                                   org.semanticweb.owlapi.model.OWLOntologyManager owlOntologyManager,
                                   org.semanticweb.owlapi.model.OWLOntology sourceOntology,
                                   org.semanticweb.owlapi.model.OWLOntology unitsOntology,
                                   org.semanticweb.owlapi.model.OWLObjectProperty viewProperty)
Parameters:
owlDataFactory -
owlOntologyManager -
sourceOntology -
unitsOntology -
viewProperty -
Method Detail

getAssertedViewOntology

public org.semanticweb.owlapi.model.OWLOntology getAssertedViewOntology()
Automatically generated Property View Ontology, containing axioms C' == P some C, for each C in source ontology

Returns:

setAssertedViewOntology

public void setAssertedViewOntology(org.semanticweb.owlapi.model.OWLOntology assertedViewOntology)

getInferredViewOntology

public org.semanticweb.owlapi.model.OWLOntology getInferredViewOntology()
Generated after running buildInferredViewOntology. Can be the same as assertedViewOntology - in which case both the assertions and the inferences go in the same ontology

Returns:

setInferredViewOntology

public void setInferredViewOntology(org.semanticweb.owlapi.model.OWLOntology inferredViewOntology)

getViewEntities

public Set<org.semanticweb.owlapi.model.OWLEntity> getViewEntities()
The set of all entities in the view ontology

Returns:

setViewEntities

public void setViewEntities(Set<org.semanticweb.owlapi.model.OWLEntity> viewEntities)

addViewEntities

public void addViewEntities(Set<org.semanticweb.owlapi.model.OWLEntity> newEntities)

getViewRootClass

public org.semanticweb.owlapi.model.OWLClass getViewRootClass()
typically [P some owl:Thing]

Returns:

getViewLabelPrefix

public String getViewLabelPrefix()

setViewLabelPrefix

public void setViewLabelPrefix(String viewLabelPrefix)

getViewLabelSuffix

public String getViewLabelSuffix()

setViewLabelSuffix

public void setViewLabelSuffix(String viewLabelSuffix)

setViewLabelPrefixAndSuffix

public void setViewLabelPrefixAndSuffix(String viewLabelPrefix,
                                        String viewLabelSuffix)

buildViewOntology

public void buildViewOntology()
                       throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

buildViewOntology

public void buildViewOntology(org.semanticweb.owlapi.model.IRI avoIRI,
                              org.semanticweb.owlapi.model.IRI ivoIRI)
                       throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Constructs view ontology (PVO) from source ontology (SO), such that every class C in SO has a corresponding view class C', such that C' == P some C The PVO imports both the SO, and the elements ontology Also prepares the inferred view ontology (IPVO) You must call buildInferredViewOntology yourself (because you need to set up the reasoner object yourself)

Parameters:
avoIRI -
ivoIRI -
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

buildInferredViewOntology

public void buildInferredViewOntology(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
Once the PVO has been constructed, this uses a reasoner to classify it. The inferred direct superclasses of all view entities are added to the IPVO In addition to classifying PVO, the elements ontology (e,g genes) is also classified.

Parameters:
reasoner -


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