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DL Queries with a real reasoner
Ignazio Palmisano edited this page May 9, 2015
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The DL Query Example class presents a DL parsing program that uses the StructuralReasoner as a reasoner.
The choice of this particular reasoner is dictated by the fact that the code is contained inside the OWL API and therefore must not contain references to libraries which are not included in the API.
However, this has confused some readers: 'how comes no results are displayed in my queries?' is a common question. The example below uses a real reasoner, HermiT, to back up the same code you can find in the DLQueryExample.java file.
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.util.Collections;
import java.util.Set;
import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser;
import org.semanticweb.HermiT.Reasoner;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.expression.OWLEntityChecker;
import org.semanticweb.owlapi.expression.ParserException;
import org.semanticweb.owlapi.expression.ShortFormEntityChecker;
import org.semanticweb.owlapi.io.StringDocumentSource;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.reasoner.Node;
import org.semanticweb.owlapi.reasoner.NodeSet;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.util.BidirectionalShortFormProvider;
import org.semanticweb.owlapi.util.BidirectionalShortFormProviderAdapter;
import org.semanticweb.owlapi.util.ShortFormProvider;
import org.semanticweb.owlapi.util.SimpleShortFormProvider;
public class DLQueriesWithHermiT {
public static void main(String[] args) throws Exception {
// Load an example ontology.
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager
.loadOntologyFromOntologyDocument(new StringDocumentSource(koala));
// We need a reasoner to do our query answering
// These two lines are the only relevant difference between this code and the original example
// This example uses HermiT: http://hermit-reasoner.com/
OWLReasoner reasoner = new Reasoner.ReasonerFactory().createReasoner(ontology);
ShortFormProvider shortFormProvider = new SimpleShortFormProvider();
// Create the DLQueryPrinter helper class. This will manage the
// parsing of input and printing of results
DLQueryPrinter dlQueryPrinter = new DLQueryPrinter(new DLQueryEngine(reasoner,
shortFormProvider), shortFormProvider);
// Enter the query loop. A user is expected to enter class
// expression on the command line.
BufferedReader br = new BufferedReader(new InputStreamReader(System.in, "UTF-8"));
while (true) {
System.out
.println("Type a class expression in Manchester Syntax and press Enter (or press x to exit):");
String classExpression = br.readLine();
// Check for exit condition
if (classExpression == null || classExpression.equalsIgnoreCase("x")) {
break;
}
dlQueryPrinter.askQuery(classExpression.trim());
System.out.println();
}
}
// for convenience, the Koala ontology is stored in this string
private final static String koala = "<?xml version=\\"1.0\\"?>\\n"
+ "<rdf:RDF xmlns:rdf=\\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\\" xmlns:rdfs=\\"http://www.w3.org/2000/01/rdf-schema#\\" xmlns:owl=\\"http://www.w3.org/2002/07/owl#\\" xmlns=\\"http://protege.stanford.edu/plugins/owl/owl-library/koala.owl#\\" xml:base=\\"http://protege.stanford.edu/plugins/owl/owl-library/koala.owl\\">\\n"
+ " <owl:Ontology rdf:about=\\"\\"/>\\n"
+ " <owl:Class rdf:ID=\\"Female\\"><owl:equivalentClass><owl:Restriction><owl:onProperty><owl:FunctionalProperty rdf:about=\\"#hasGender\\"/></owl:onProperty><owl:hasValue><Gender rdf:ID=\\"female\\"/></owl:hasValue></owl:Restriction></owl:equivalentClass></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"Marsupials\\"><owl:disjointWith><owl:Class rdf:about=\\"#Person\\"/></owl:disjointWith><rdfs:subClassOf><owl:Class rdf:about=\\"#Animal\\"/></rdfs:subClassOf></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"Student\\"><owl:equivalentClass><owl:Class><owl:intersectionOf rdf:parseType=\\"Collection\\"><owl:Class rdf:about=\\"#Person\\"/><owl:Restriction><owl:onProperty><owl:FunctionalProperty rdf:about=\\"#isHardWorking\\"/></owl:onProperty><owl:hasValue rdf:datatype=\\"http://www.w3.org/2001/XMLSchema#boolean\\">true</owl:hasValue></owl:Restriction><owl:Restriction><owl:someValuesFrom><owl:Class rdf:about=\\"#University\\"/></owl:someValuesFrom><owl:onProperty><owl:ObjectProperty rdf:about=\\"#hasHabitat\\"/></owl:onProperty></owl:Restriction></owl:intersectionOf></owl:Class></owl:equivalentClass></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"KoalaWithPhD\\"><owl:versionInfo>1.2</owl:versionInfo><owl:equivalentClass><owl:Class><owl:intersectionOf rdf:parseType=\\"Collection\\"><owl:Restriction><owl:hasValue><Degree rdf:ID=\\"PhD\\"/></owl:hasValue><owl:onProperty><owl:ObjectProperty rdf:about=\\"#hasDegree\\"/></owl:onProperty></owl:Restriction><owl:Class rdf:about=\\"#Koala\\"/></owl:intersectionOf></owl:Class></owl:equivalentClass></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"University\\"><rdfs:subClassOf><owl:Class rdf:ID=\\"Habitat\\"/></rdfs:subClassOf></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"Koala\\"><rdfs:subClassOf><owl:Restriction><owl:hasValue rdf:datatype=\\"http://www.w3.org/2001/XMLSchema#boolean\\">false</owl:hasValue><owl:onProperty><owl:FunctionalProperty rdf:about=\\"#isHardWorking\\"/></owl:onProperty></owl:Restriction></rdfs:subClassOf><rdfs:subClassOf><owl:Restriction><owl:someValuesFrom><owl:Class rdf:about=\\"#DryEucalyptForest\\"/></owl:someValuesFrom><owl:onProperty><owl:ObjectProperty rdf:about=\\"#hasHabitat\\"/></owl:onProperty></owl:Restriction></rdfs:subClassOf><rdfs:subClassOf rdf:resource=\\"#Marsupials\\"/></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"Animal\\"><rdfs:seeAlso>Male</rdfs:seeAlso><rdfs:subClassOf><owl:Restriction><owl:onProperty><owl:ObjectProperty rdf:about=\\"#hasHabitat\\"/></owl:onProperty><owl:minCardinality rdf:datatype=\\"http://www.w3.org/2001/XMLSchema#int\\">1</owl:minCardinality></owl:Restriction></rdfs:subClassOf><rdfs:subClassOf><owl:Restriction><owl:cardinality rdf:datatype=\\"http://www.w3.org/2001/XMLSchema#int\\">1</owl:cardinality><owl:onProperty><owl:FunctionalProperty rdf:about=\\"#hasGender\\"/></owl:onProperty></owl:Restriction></rdfs:subClassOf><owl:versionInfo>1.1</owl:versionInfo></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"Forest\\"><rdfs:subClassOf rdf:resource=\\"#Habitat\\"/></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"Rainforest\\"><rdfs:subClassOf rdf:resource=\\"#Forest\\"/></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"GraduateStudent\\"><rdfs:subClassOf><owl:Restriction><owl:onProperty><owl:ObjectProperty rdf:about=\\"#hasDegree\\"/></owl:onProperty><owl:someValuesFrom><owl:Class><owl:oneOf rdf:parseType=\\"Collection\\"><Degree rdf:ID=\\"BA\\"/><Degree rdf:ID=\\"BS\\"/></owl:oneOf></owl:Class></owl:someValuesFrom></owl:Restriction></rdfs:subClassOf><rdfs:subClassOf rdf:resource=\\"#Student\\"/></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"Parent\\"><owl:equivalentClass><owl:Class><owl:intersectionOf rdf:parseType=\\"Collection\\"><owl:Class rdf:about=\\"#Animal\\"/><owl:Restriction><owl:onProperty><owl:ObjectProperty rdf:about=\\"#hasChildren\\"/></owl:onProperty><owl:minCardinality rdf:datatype=\\"http://www.w3.org/2001/XMLSchema#int\\">1</owl:minCardinality></owl:Restriction></owl:intersectionOf></owl:Class></owl:equivalentClass><rdfs:subClassOf rdf:resource=\\"#Animal\\"/></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"DryEucalyptForest\\"><rdfs:subClassOf rdf:resource=\\"#Forest\\"/></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"Quokka\\"><rdfs:subClassOf><owl:Restriction><owl:hasValue rdf:datatype=\\"http://www.w3.org/2001/XMLSchema#boolean\\">true</owl:hasValue><owl:onProperty><owl:FunctionalProperty rdf:about=\\"#isHardWorking\\"/></owl:onProperty></owl:Restriction></rdfs:subClassOf><rdfs:subClassOf rdf:resource=\\"#Marsupials\\"/></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"TasmanianDevil\\"><rdfs:subClassOf rdf:resource=\\"#Marsupials\\"/></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"MaleStudentWith3Daughters\\"><owl:equivalentClass><owl:Class><owl:intersectionOf rdf:parseType=\\"Collection\\"><owl:Class rdf:about=\\"#Student\\"/><owl:Restriction><owl:onProperty><owl:FunctionalProperty rdf:about=\\"#hasGender\\"/></owl:onProperty><owl:hasValue><Gender rdf:ID=\\"male\\"/></owl:hasValue></owl:Restriction><owl:Restriction><owl:onProperty><owl:ObjectProperty rdf:about=\\"#hasChildren\\"/></owl:onProperty><owl:cardinality rdf:datatype=\\"http://www.w3.org/2001/XMLSchema#int\\">3</owl:cardinality></owl:Restriction><owl:Restriction><owl:allValuesFrom rdf:resource=\\"#Female\\"/><owl:onProperty><owl:ObjectProperty rdf:about=\\"#hasChildren\\"/></owl:onProperty></owl:Restriction></owl:intersectionOf></owl:Class></owl:equivalentClass></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"Degree\\"/>\\n"
+ " <owl:Class rdf:ID=\\"Male\\"><owl:equivalentClass><owl:Restriction><owl:hasValue rdf:resource=\\"#male\\"/><owl:onProperty><owl:FunctionalProperty rdf:about=\\"#hasGender\\"/></owl:onProperty></owl:Restriction></owl:equivalentClass></owl:Class>\\n"
+ " <owl:Class rdf:ID=\\"Gender\\"/>\\n"
+ " <owl:Class rdf:ID=\\"Person\\"><rdfs:subClassOf rdf:resource=\\"#Animal\\"/><owl:disjointWith rdf:resource=\\"#Marsupials\\"/></owl:Class>\\n"
+ " <owl:ObjectProperty rdf:ID=\\"hasHabitat\\"><rdfs:range rdf:resource=\\"#Habitat\\"/><rdfs:domain rdf:resource=\\"#Animal\\"/></owl:ObjectProperty>\\n"
+ " <owl:ObjectProperty rdf:ID=\\"hasDegree\\"><rdfs:domain rdf:resource=\\"#Person\\"/><rdfs:range rdf:resource=\\"#Degree\\"/></owl:ObjectProperty>\\n"
+ " <owl:ObjectProperty rdf:ID=\\"hasChildren\\"><rdfs:range rdf:resource=\\"#Animal\\"/><rdfs:domain rdf:resource=\\"#Animal\\"/></owl:ObjectProperty>\\n"
+ " <owl:FunctionalProperty rdf:ID=\\"hasGender\\"><rdfs:range rdf:resource=\\"#Gender\\"/><rdf:type rdf:resource=\\"http://www.w3.org/2002/07/owl#ObjectProperty\\"/><rdfs:domain rdf:resource=\\"#Animal\\"/></owl:FunctionalProperty>\\n"
+ " <owl:FunctionalProperty rdf:ID=\\"isHardWorking\\"><rdfs:range rdf:resource=\\"http://www.w3.org/2001/XMLSchema#boolean\\"/><rdfs:domain rdf:resource=\\"#Person\\"/><rdf:type rdf:resource=\\"http://www.w3.org/2002/07/owl#DatatypeProperty\\"/></owl:FunctionalProperty>\\n"
+ " <Degree rdf:ID=\\"MA\\"/>\\n" + "</rdf:RDF>";
}
class DLQueryEngine {
private final OWLReasoner reasoner;
private final DLQueryParser parser;
public DLQueryEngine(OWLReasoner reasoner, ShortFormProvider shortFormProvider) {
this.reasoner = reasoner;
parser = new DLQueryParser(reasoner.getRootOntology(), shortFormProvider);
}
public Set<OWLClass> getSuperClasses(String classExpressionString, boolean direct) {
if (classExpressionString.trim().length() == 0) {
return Collections.emptySet();
}
OWLClassExpression classExpression = parser
.parseClassExpression(classExpressionString);
NodeSet<OWLClass> superClasses = reasoner
.getSuperClasses(classExpression, direct);
return superClasses.getFlattened();
}
public Set<OWLClass> getEquivalentClasses(String classExpressionString) {
if (classExpressionString.trim().length() == 0) {
return Collections.emptySet();
}
OWLClassExpression classExpression = parser
.parseClassExpression(classExpressionString);
Node<OWLClass> equivalentClasses = reasoner.getEquivalentClasses(classExpression);
Set<OWLClass> result = null;
if (classExpression.isAnonymous()) {
result = equivalentClasses.getEntities();
} else {
result = equivalentClasses.getEntitiesMinus(classExpression.asOWLClass());
}
return result;
}
public Set<OWLClass> getSubClasses(String classExpressionString, boolean direct) {
if (classExpressionString.trim().length() == 0) {
return Collections.emptySet();
}
OWLClassExpression classExpression = parser
.parseClassExpression(classExpressionString);
NodeSet<OWLClass> subClasses = reasoner.getSubClasses(classExpression, direct);
return subClasses.getFlattened();
}
public Set<OWLNamedIndividual> getInstances(String classExpressionString,
boolean direct) {
if (classExpressionString.trim().length() == 0) {
return Collections.emptySet();
}
OWLClassExpression classExpression = parser
.parseClassExpression(classExpressionString);
NodeSet<OWLNamedIndividual> individuals = reasoner.getInstances(classExpression,
direct);
return individuals.getFlattened();
}
}
class DLQueryParser {
private final OWLOntology rootOntology;
private final BidirectionalShortFormProvider bidiShortFormProvider;
public DLQueryParser(OWLOntology rootOntology, ShortFormProvider shortFormProvider) {
this.rootOntology = rootOntology;
OWLOntologyManager manager = rootOntology.getOWLOntologyManager();
Set<OWLOntology> importsClosure = rootOntology.getImportsClosure();
// Create a bidirectional short form provider to do the actual mapping.
// It will generate names using the input
// short form provider.
bidiShortFormProvider = new BidirectionalShortFormProviderAdapter(manager,
importsClosure, shortFormProvider);
}
public OWLClassExpression parseClassExpression(String classExpressionString) {
OWLDataFactory dataFactory = rootOntology.getOWLOntologyManager()
.getOWLDataFactory();
ManchesterOWLSyntaxEditorParser parser = new ManchesterOWLSyntaxEditorParser(
dataFactory, classExpressionString);
parser.setDefaultOntology(rootOntology);
OWLEntityChecker entityChecker = new ShortFormEntityChecker(bidiShortFormProvider);
parser.setOWLEntityChecker(entityChecker);
return parser.parseClassExpression();
}
}
class DLQueryPrinter {
private final DLQueryEngine dlQueryEngine;
private final ShortFormProvider shortFormProvider;
public DLQueryPrinter(DLQueryEngine engine, ShortFormProvider shortFormProvider) {
this.shortFormProvider = shortFormProvider;
dlQueryEngine = engine;
}
public void askQuery(String classExpression) {
if (classExpression.length() == 0) {
System.out.println("No class expression specified");
} else {
try {
StringBuilder sb = new StringBuilder();
sb.append("\\nQUERY: ").append(classExpression).append("\\n\\n");
Set<OWLClass> superClasses = dlQueryEngine.getSuperClasses(
classExpression, false);
printEntities("SuperClasses", superClasses, sb);
Set<OWLClass> equivalentClasses = dlQueryEngine
.getEquivalentClasses(classExpression);
printEntities("EquivalentClasses", equivalentClasses, sb);
Set<OWLClass> subClasses = dlQueryEngine.getSubClasses(classExpression,
true);
printEntities("SubClasses", subClasses, sb);
Set<OWLNamedIndividual> individuals = dlQueryEngine.getInstances(
classExpression, true);
printEntities("Instances", individuals, sb);
System.out.println(sb.toString());
} catch (ParserException e) {
System.out.println(e.getMessage());
}
}
}
private void printEntities(String name, Set<? extends OWLEntity> entities,
StringBuilder sb) {
sb.append(name);
int length = 50 - name.length();
for (int i = 0; i < length; i++) {
sb.append(".");
}
sb.append("\\n\\n");
if (!entities.isEmpty()) {
for (OWLEntity entity : entities) {
sb.append("\\t").append(shortFormProvider.getShortForm(entity))
.append("\\n");
}
} else {
sb.append("\\t[NONE]\\n");
}
sb.append("\\n");
}
}