owltools

Class InferenceBuilder

java.lang.Object

owltools.InferenceBuilder

public class InferenceBuilder
extends Object

This class build inferred axioms of an ontology.

Author:

Shahid Manzoor

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	InferenceBuilder.ConsistencyReport
static interface	InferenceBuilder.OWLClassFilter Filter for relevant OWLClasses during the inference Building process.
static class	InferenceBuilder.PotentialRedundant

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.apache.log4j.Logger	logger
static String	REASONER_ELK
static String	REASONER_HERMIT
static String	REASONER_JCEL
static String	REASONER_JFACT
static String	REASONER_MORE
static String	REASONER_MORE_HERMIT
static String	REASONER_MORE_JFACT

Constructor Summary

Constructors

Constructor and Description
InferenceBuilder(OWLGraphWrapper graph)
InferenceBuilder(OWLGraphWrapper graph, org.semanticweb.owlapi.reasoner.OWLReasonerFactory factory, boolean enforceEL)
InferenceBuilder(OWLGraphWrapper graph, String reasonerName)
InferenceBuilder(OWLGraphWrapper graph, String reasonerName, boolean enforceEL)

Method Summary

Methods

Modifier and Type	Method and Description
void	addFilter(InferenceBuilder.OWLClassFilter filter)
List<org.semanticweb.owlapi.model.OWLAxiom>	buildInferences()
List<org.semanticweb.owlapi.model.OWLAxiom>	buildInferences(boolean alwaysAssertSuperClasses) if alwaysAssertSuperClasses then ensure that superclasses are always asserted for every equivalence axiom, except in the case where a more specific superclass is already in the set of inferences.
List<InferenceBuilder.PotentialRedundant>	checkPotentialRedundantSubClassAxioms() Check all classes for potential redundant subClass axioms of type:
List<InferenceBuilder.PotentialRedundant>	checkPotentialRedundantSubClassAxioms(Collection<? extends org.semanticweb.owlapi.model.OWLAxiom> inferredAxioms) Check the list of axioms for potential redundant subClass axioms of type:
void	clearFilters()
void	dispose() Dispose the internal reasoner
protected boolean	doInferencesForClass(org.semanticweb.owlapi.model.OWLClass cls, org.semanticweb.owlapi.model.OWLOntology ont) Only create inferences for an OWLClass, if this method returns true.
static OWLGraphWrapper	enforceEL(OWLGraphWrapper graph)
static OWLGraphWrapper	enforceEL(OWLGraphWrapper graph, org.semanticweb.owlapi.model.IRI elOntologyIRI) Create an ontology with EL as description logic profile.
List<org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom>	getEquivalentNamedClassPairs()
Set<Set<org.semanticweb.owlapi.model.OWLAxiom>>	getExplaination(String c1, String c2, OWLQuantifiedProperty.Quantifier quantifier)
static org.semanticweb.owlapi.reasoner.OWLReasonerFactory	getFactory(String reasonerName)
OWLGraphWrapper	getOWLGraphWrapper()
org.semanticweb.owlapi.reasoner.OWLReasoner	getReasoner(org.semanticweb.owlapi.model.OWLOntology ontology)
Collection<org.semanticweb.owlapi.model.OWLAxiom>	getRedundantAxioms()
protected Set<org.semanticweb.owlapi.model.OWLAxiom>	getRedundantAxioms(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, org.semanticweb.owlapi.model.OWLDataFactory dataFactory) Search for redundant axioms.
protected boolean	hasAssertedSubClassAxiom(org.semanticweb.owlapi.model.OWLClass subClass, org.semanticweb.owlapi.model.OWLClassExpression superClass, org.semanticweb.owlapi.model.OWLOntology ontology) Check the ontology for an existing subClassOf axiom with the given sub- and superclass.
protected boolean	isDebug()
protected void	logDebug(String msg)
protected void	logInfo(String msg)
InferenceBuilder.ConsistencyReport	performConsistencyChecks()
void	removeFilter(InferenceBuilder.OWLClassFilter filter)
void	setOWLGraphWrapper(OWLGraphWrapper g)
void	setReasoner(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
protected static void	updateRedundant(org.semanticweb.owlapi.model.OWLClass cls, org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLAxiom> redundantAxioms, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, org.semanticweb.owlapi.model.OWLDataFactory dataFactory) Update the set of redundant axioms for the given OWLClass cls.

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

REASONER_HERMIT

public static final String REASONER_HERMIT

See Also:

Constant Field Values

REASONER_JCEL

public static final String REASONER_JCEL

See Also:

Constant Field Values

REASONER_ELK

public static final String REASONER_ELK

See Also:

Constant Field Values

REASONER_JFACT

public static final String REASONER_JFACT

See Also:

Constant Field Values

REASONER_MORE

public static final String REASONER_MORE

See Also:

Constant Field Values

REASONER_MORE_HERMIT

public static final String REASONER_MORE_HERMIT

See Also:

Constant Field Values

REASONER_MORE_JFACT

public static final String REASONER_MORE_JFACT

See Also:

Constant Field Values

Constructor Detail

InferenceBuilder

public InferenceBuilder(OWLGraphWrapper graph)

InferenceBuilder

public InferenceBuilder(OWLGraphWrapper graph,
                String reasonerName)

InferenceBuilder

public InferenceBuilder(OWLGraphWrapper graph,
                String reasonerName,
                boolean enforceEL)

InferenceBuilder

public InferenceBuilder(OWLGraphWrapper graph,
                org.semanticweb.owlapi.reasoner.OWLReasonerFactory factory,
                boolean enforceEL)

Method Detail

getFactory

public static org.semanticweb.owlapi.reasoner.OWLReasonerFactory getFactory(String reasonerName)

enforceEL

public static OWLGraphWrapper enforceEL(OWLGraphWrapper graph)

enforceEL

public static OWLGraphWrapper enforceEL(OWLGraphWrapper graph,
                        org.semanticweb.owlapi.model.IRI elOntologyIRI)

Create an ontology with EL as description logic profile. This is achieved by removing the non-compatible axioms. WARNING: Due to the data type restrictions of EL, all deprecation annotations are removed in this process.

Parameters:

graph -

elOntologyIRI -

Returns:

ontology limited to EL

addFilter

public void addFilter(InferenceBuilder.OWLClassFilter filter)

removeFilter

public void removeFilter(InferenceBuilder.OWLClassFilter filter)

clearFilters

public void clearFilters()

getOWLGraphWrapper

public OWLGraphWrapper getOWLGraphWrapper()

setOWLGraphWrapper

public void setOWLGraphWrapper(OWLGraphWrapper g)

setReasoner

public void setReasoner(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)

getReasoner

public org.semanticweb.owlapi.reasoner.OWLReasoner getReasoner(org.semanticweb.owlapi.model.OWLOntology ontology)

getRedundantAxioms

public Collection<org.semanticweb.owlapi.model.OWLAxiom> getRedundantAxioms()

getEquivalentNamedClassPairs

public List<org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom> getEquivalentNamedClassPairs()

buildInferences

public List<org.semanticweb.owlapi.model.OWLAxiom> buildInferences()

buildInferences

public List<org.semanticweb.owlapi.model.OWLAxiom> buildInferences(boolean alwaysAssertSuperClasses)

if alwaysAssertSuperClasses then ensure that superclasses are always asserted for every equivalence axiom, except in the case where a more specific superclass is already in the set of inferences. this is because applications - particularly obof-centered ones - ignore equivalence axioms by default side effects: sets redundantAxioms (@see #getRedundantAxioms())

Parameters:

alwaysAssertSuperClasses -

Returns:

inferred axioms

doInferencesForClass

protected boolean doInferencesForClass(org.semanticweb.owlapi.model.OWLClass cls,
                           org.semanticweb.owlapi.model.OWLOntology ont)

Only create inferences for an OWLClass, if this method returns true.

Parameters:

cls -

ont -

Returns:

boolean

hasAssertedSubClassAxiom

protected boolean hasAssertedSubClassAxiom(org.semanticweb.owlapi.model.OWLClass subClass,
                               org.semanticweb.owlapi.model.OWLClassExpression superClass,
                               org.semanticweb.owlapi.model.OWLOntology ontology)

Check the ontology for an existing subClassOf axiom with the given sub- and superclass. This search ignores axiom annotations (i.e. is_inferred=true). WARNING: Do not use OWLOntology.containsAxiomIgnoreAnnotations(OWLAxiom) In the current OWL-API, this seems to be very very slow.

Parameters:

subClass -

superClass -

ontology -

Returns:

true, if there is an axiom for this subClass statement.

getRedundantAxioms

protected Set<org.semanticweb.owlapi.model.OWLAxiom> getRedundantAxioms(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                            org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                                                            org.semanticweb.owlapi.model.OWLDataFactory dataFactory)

Search for redundant axioms.

Parameters:

ontology -

reasoner -

dataFactory -

Returns:

set of all redundant axioms

updateRedundant

protected static void updateRedundant(org.semanticweb.owlapi.model.OWLClass cls,
                   org.semanticweb.owlapi.model.OWLOntology ontology,
                   Set<org.semanticweb.owlapi.model.OWLAxiom> redundantAxioms,
                   org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                   org.semanticweb.owlapi.model.OWLDataFactory dataFactory)

Update the set of redundant axioms for the given OWLClass cls.

Parameters:

cls -

ontology -

redundantAxioms -

reasoner -

dataFactory -

performConsistencyChecks

public InferenceBuilder.ConsistencyReport performConsistencyChecks()

checkPotentialRedundantSubClassAxioms

public List<InferenceBuilder.PotentialRedundant> checkPotentialRedundantSubClassAxioms(Collection<? extends org.semanticweb.owlapi.model.OWLAxiom> inferredAxioms)

Check the list of axioms for potential redundant subClass axioms of type:

   A SubClassOf R some B
    and
   A SubClassOf B
 

Parameters:

inferredAxioms -

Returns:

list of axiom pairs

checkPotentialRedundantSubClassAxioms

public List<InferenceBuilder.PotentialRedundant> checkPotentialRedundantSubClassAxioms()

Check all classes for potential redundant subClass axioms of type:

   A SubClassOf R some B
    and
   A SubClassOf B
 

Returns:

list of axiom pairs

getExplaination

public Set<Set<org.semanticweb.owlapi.model.OWLAxiom>> getExplaination(String c1,
                                                              String c2,
                                                              OWLQuantifiedProperty.Quantifier quantifier)

dispose

public void dispose()

Dispose the internal reasoner

logInfo

protected void logInfo(String msg)

isDebug

protected boolean isDebug()

logDebug

protected void logDebug(String msg)