Pellet internalReasonerException in OWL API
林雅
Have been stuck one day and would someone be kind enough to help?
I have loaded an ontology which imported SWEET(Semantic Web for Earth and Environmental Ontology). I did some SPARQL query on it, and I got such answer: "Object Property hasLowerBound is used with a hasValue restriction where the value is a literal: "0"^^integer". (hasLowerBound, which I have checked in the SWEET, is an Datatype Ontology in SWEET)
How can I solve this problem?
Here is the code I wrote and the error I got,Thank you so much for your help~
package loadOnto;
//import static org.semanticweb.owlapi.search.EntitySearcher.getAnnotationObjects;
//import static org.semanticweb.owlapi.search.Searcher.annotationObjects;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.util.*;
import javax.annotation.Nonnull;
import org.semanticweb.owlapi.apibinding.OWLManager;
//import org.semanticweb.owlapi.formats.OWLXMLDocumentFormat;
import org.semanticweb.owlapi.io.StreamDocumentTarget;
import org.semanticweb.owlapi.io.StringDocumentSource;
import org.semanticweb.owlapi.io.StringDocumentTarget;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.profiles.OWL2DLProfile;
import org.semanticweb.owlapi.profiles.OWLProfileReport;
import org.semanticweb.owlapi.profiles.OWLProfileViolation;
import org.semanticweb.owlapi.reasoner.*;
import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory;
import org.semanticweb.owlapi.util.*;
import org.semanticweb.owlapi.vocab.OWL2Datatype;
import org.semanticweb.owlapi.vocab.OWLFacet;
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import com.clarkparsia.pellet.sparqldl.jena.SparqlDLExecutionFactory;
import com.clarkparsia.pellet.sparqldl.model.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.model.InfModel;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import uk.ac.manchester.cs.owlapi.modularity.ModuleType;
import uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor;
public class load {
public static void main(String[] args) throws OWLOntologyCreationException {
// Get hold of an ontology manager
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
// We can also load ontologies from files. Create a file object that points to the local copy
File file = new File("G:/Protege/owlfiles/sweetAll.owl");
// Load the local copy
OWLOntology loadMODIS = manager.loadOntologyFromOntologyDocument(file);
PelletReasoner reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner( loadMODIS );
System.out.println("CheckParsing.should() " + reasoner.isConsistent());
System.out.println("Loaded ontology: " + loadMODIS);
}
}
Error
Exception in thread "main" org.mindswap.pellet.exceptions.InternalReasonerException: Object Property hasLowerBound is used with a hasValue restriction where the value is a literal: "0"^^integer at org.mindswap.pellet.tableau.completion.rule.SomeValuesRule.applySomeValuesRule(SomeValuesRule.java:204) at org.mindswap.pellet.tableau.completion.rule.SomeValuesRule.apply(SomeValuesRule.java:64) at org.mindswap.pellet.tableau.completion.rule.AbstractTableauRule.apply(AbstractTableauRule.java:64) at org.mindswap.pellet.tableau.completion.SROIQStrategy.complete(SROIQStrategy.java:157) at org.mindswap.pellet.ABox.isConsistent(ABox.java:1423) at org.mindswap.pellet.ABox.isConsistent(ABox.java:1260) at org.mindswap.pellet.KnowledgeBase.consistency(KnowledgeBase.java:1987) at org.mindswap.pellet.KnowledgeBase.isConsistent(KnowledgeBase.java:2061) at org.mindswap.pellet.jena.PelletInfGraph.prepare(PelletInfGraph.java:258) at org.mindswap.pellet.jena.PelletInfGraph.prepare(PelletInfGraph.java:241) at com.clarkparsia.pellet.sparqldl.jena.SparqlDLExecutionFactory.create(SparqlDLExecutionFactory.java:113) at com.clarkparsia.pellet.sparqldl.jena.SparqlDLExecutionFactory.create(SparqlDLExecutionFactory.java:261) at com.clarkparsia.pellet.sparqldl.jena.SparqlDLExecutionFactory.create(SparqlDLExecutionFactory.java:226) at loadMODIS.load.main(load.java:78)
Attached is the ontology I've been reason on.
Thank you very much for your kind help!
林雅
在 2016年1月23日星期六 UTC+8下午5:36:38，林雅写道：
Ignazio Palmisano
> Here is the version information:
>
> Version of Pellet: 2.3.0 Version of OWL API: 3.4.10
Pellet is checking for a data property case and assumes that if a
property is not a data property it must be an object property. This is
always the case for OWL 2 ontologies, but this ontology is not being
parsed as an OWL 2 compatible ontology - punning of an annotation
property and a data property is not allowed.
I'm not sure yet whether the problem is in the ontology or in the
OWLAPI parsing of it.
Edit: It's a parsing issue. hasLowerBound is declared in relaMath.owl
as data property. However relaMath.owl imports reprMath.owl, which
uses hasLowerBound but does not declare it. reprMath.owl imports
relaMath.owl, so there is a cyclic import there.
The problem is that, during parsing: - relaMath.owl is parsed, import
is found, reprMath.owl import is resolved; no declarations are parsed
yet. - reprMath.owl is parsed, import is found. relaMath.owl is
already being parsed, so call does nothing. All entities declared in
relaMath.owl are included while parsing reprMath.owl. PROBLEM: the
entities have not been parsed yet, so this set is empty. hasLowerBound
is found in reprMath but no declaration exists yet. Therefore OWLAPI
defaults to AnnotationProperty. - relaMath.owl parsing continues,
declaration is found.
Final result: Any ontology importing relaMath.owl has illegal punning
for hasLowerBound. OWLAPI bug.
Workaround: Add data property declaration to reprMath.owl:
<owl:DatatypeProperty rdf:about="#hasLowerBound"/>
This might need to be done in more than one ontology. The bug affects
all OWLAPI versions.
Cheers,
I.
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Ignazio Palmisano
> On 23 January 2016 at 09:40, 林雅 <julya...@gmail.com> wrote:
>> Here is the version information:
>>
>> Version of Pellet: 2.3.0 Version of OWL API: 3.4.10
>
>
> hasLowerBound is parsed as a data property and an annotation property.
underlying issue.
I.
林雅
在 2016年1月23日星期六 UTC+8下午5:36:38，林雅写道：
Have been stuck one day and would someone be kind enough to help?