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Revisit parents/children of terms to make sure none were missed
When using a limited reasoner (i.e. transitive, OWL micro/mini), some of the ancestors or descendants of a term may be missed. To compensate for that, do a few additional direct checks.
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‎src/ubic/basecode/ontology/jena/JenaUtils.java‎

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Original file line numberDiff line numberDiff line change
@@ -8,6 +8,8 @@
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import com.hp.hpl.jena.util.iterator.Filter;
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import com.hp.hpl.jena.util.iterator.UniqueExtendedIterator;
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import org.apache.commons.lang3.time.StopWatch;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import javax.annotation.Nullable;
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import java.util.*;
@@ -18,7 +20,25 @@
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class JenaUtils {
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protected static Logger log = LoggerFactory.getLogger( JenaUtils.class );
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public static Collection<OntClass> getParents( OntModel model, Collection<OntClass> ontClasses, boolean direct, @Nullable Set<Restriction> additionalRestrictions ) {
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Collection<OntClass> parents = getParentsInternal( model, ontClasses, direct, additionalRestrictions );
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if ( shouldRevisit( parents, direct, model, additionalRestrictions ) ) {
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// if there are some missing direct parents, revisit the hierarchy
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Set<OntClass> parentsToRevisit = new HashSet<>( parents );
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while ( !parentsToRevisit.isEmpty() ) {
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log.debug( "Revisiting the direct parents of {} terms...", parentsToRevisit.size() );
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parentsToRevisit = new HashSet<>( getParentsInternal( model, parentsToRevisit, true, additionalRestrictions ) );
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parentsToRevisit.removeAll( parents );
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log.debug( "Found {} missed parents.", parentsToRevisit.size() );
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parents.addAll( parentsToRevisit );
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}
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}
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return parents;
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}
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private static Collection<OntClass> getParentsInternal( OntModel model, Collection<OntClass> ontClasses, boolean direct, @Nullable Set<Restriction> additionalRestrictions ) {
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ontClasses = ontClasses.stream()
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.map( t -> t.inModel( model ) )
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.filter( t -> t.canAs( OntClass.class ) )
@@ -65,6 +85,22 @@ public static Collection<OntClass> getParents( OntModel model, Collection<OntCla
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}
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public static Collection<OntClass> getChildren( OntModel model, Collection<OntClass> terms, boolean direct, @Nullable Set<Restriction> additionalRestrictions ) {
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Collection<OntClass> children = getChildrenInternal( model, terms, direct, additionalRestrictions );
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if ( shouldRevisit( children, direct, model, additionalRestrictions ) ) {
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// if there are some missing direct children, revisit the hierarchy
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Set<OntClass> childrenToRevisit = new HashSet<>( children );
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while ( !childrenToRevisit.isEmpty() ) {
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log.debug( "Revisiting the direct parents of {} terms...", childrenToRevisit.size() );
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childrenToRevisit = new HashSet<>( JenaUtils.getChildrenInternal( model, childrenToRevisit, true, additionalRestrictions ) );
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childrenToRevisit.removeAll( children );
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log.debug( "Found {} missed children.", childrenToRevisit.size() );
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children.addAll( childrenToRevisit );
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}
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}
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return children;
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}
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public static Collection<OntClass> getChildrenInternal( OntModel model, Collection<OntClass> terms, boolean direct, @Nullable Set<Restriction> additionalRestrictions ) {
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terms = terms.stream()
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.map( t -> t.inModel( model ) )
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.filter( t -> t.canAs( OntClass.class ) )
@@ -103,6 +139,42 @@ public static Collection<OntClass> getChildren( OntModel model, Collection<OntCl
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return result;
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}
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/**
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* Check if a set of terms should be revisited to find missing parents or children.
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* <p>
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* To be considered, the model must have a reasoner that lacks one of {@code rdfs:subClassOf}, {@code owl:subValuesFrom}
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* or {@code owl:allValuesFrom} inference capabilities. If a model has no reasoner, revisiting is not desirable and
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* thus this will return false.
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* <p>
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* If direct is false or terms is empty, it's not worth revisiting.
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*/
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private static boolean shouldRevisit( Collection<OntClass> terms, boolean direct, OntModel model, @Nullable Set<Restriction> additionalRestrictions ) {
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return !direct
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&& !terms.isEmpty()
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&& additionalRestrictions != null
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&& model.getReasoner() != null
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&& ( !supportsSubClassInference( model ) || !supportsAdditionalRestrictionsInference( model ) );
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}
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/**
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* Check if an ontology model supports inference of {@code rdfs:subClassOf}.
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*/
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public static boolean supportsSubClassInference( OntModel model ) {
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return model.getReasoner() != null
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&& model.getReasoner().supportsProperty( model.getProfile().SUB_CLASS_OF() );
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}
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/**
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* Checks if an ontology model supports inference of with additional restrictions.
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* <p>
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* This covers {@code owl:subValuesFrom} and {@code owl:allValuesFrom} restrictions.
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*/
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public static boolean supportsAdditionalRestrictionsInference( OntModel model ) {
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return model.getReasoner() != null
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&& model.getReasoner().supportsProperty( model.getProfile().SOME_VALUES_FROM() )
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&& model.getReasoner().supportsProperty( model.getProfile().ALL_VALUES_FROM() );
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}
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public static Resource getRestrictionValue( Restriction r ) {
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if ( r.isSomeValuesFromRestriction() ) {
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return r.asSomeValuesFromRestriction().getSomeValuesFrom();

‎test/ubic/basecode/ontology/OntologyTermTest.java‎

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -14,19 +14,16 @@
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*/
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package ubic.basecode.ontology;
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import com.hp.hpl.jena.vocabulary.OWL2;
1817
import org.apache.commons.lang3.StringUtils;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import ubic.basecode.ontology.model.OntologyTerm;
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import ubic.basecode.ontology.providers.*;
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import ubic.basecode.ontology.search.OntologySearchException;
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import ubic.basecode.ontology.providers.CellLineOntologyService;
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import ubic.basecode.ontology.providers.DiseaseOntologyService;
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import ubic.basecode.ontology.providers.NIFSTDOntologyService;
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import java.io.IOException;
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import java.io.InputStream;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.zip.GZIPInputStream;
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@@ -111,7 +108,7 @@ public void testGetChildrenHasProperPart() throws Exception {
111108
assertTrue( c.contains( t1 ) );
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Collection<OntologyTerm> c2 = t.getChildren( false );
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assertEquals( 6, c2.size() );
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assertEquals( 7, c2.size() );
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OntologyTerm t2 = s.getTerm( "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_4037" );
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assertNotNull( t2 );
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assertTrue( c.contains( t2 ) );
@@ -199,7 +196,7 @@ public void testGetParentsHasProperPart() throws Exception {
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// Diencephalon [birnlex_1503] x
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Collection<OntologyTerm> parents2 = t.getParents( false );
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assertEquals( 7, parents2.size() );
199+
assertEquals( 14, parents2.size() );
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// does not includes 'continuant' and 'independent continuant' or parents of those terms.
205202
assertFalse( parents2.contains( s.getTerm( "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_1503" ) ) );

‎test/ubic/basecode/ontology/jena/JenaUtilsTest.java‎

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@@ -0,0 +1,42 @@
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package ubic.basecode.ontology.jena;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntModelSpec;
5+
import com.hp.hpl.jena.rdf.model.ModelFactory;
6+
import org.junit.Test;
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8+
import static org.junit.Assert.*;
9+
import static ubic.basecode.ontology.jena.JenaUtils.supportsAdditionalRestrictionsInference;
10+
import static ubic.basecode.ontology.jena.JenaUtils.supportsSubClassInference;
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12+
public class JenaUtilsTest {
13+
@Test
14+
public void testInferenceCapabilities() {
15+
OntModel model;
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model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );
18+
assertNull( model.getReasoner() );
19+
assertFalse( supportsSubClassInference( model ) );
20+
assertFalse( supportsAdditionalRestrictionsInference( model ) );
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model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM_TRANS_INF );
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assertNotNull( model.getReasoner() );
24+
assertTrue( supportsSubClassInference( model ) );
25+
assertFalse( supportsAdditionalRestrictionsInference( model ) );
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27+
model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM_MICRO_RULE_INF );
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assertNotNull( model.getReasoner() );
29+
assertTrue( supportsSubClassInference( model ) );
30+
assertFalse( supportsAdditionalRestrictionsInference( model ) );
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32+
model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM_MINI_RULE_INF );
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assertNotNull( model.getReasoner() );
34+
assertTrue( supportsSubClassInference( model ) );
35+
assertFalse( supportsAdditionalRestrictionsInference( model ) );
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37+
model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM_RULE_INF );
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assertNotNull( model.getReasoner() );
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assertTrue( supportsSubClassInference( model ) );
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assertTrue( supportsAdditionalRestrictionsInference( model ) );
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}
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}

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