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arteymixarteymix
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Add 'part of' and 'has part' to the set of properties allowed in inference
1 parent 2c85108 commit 4360045

1 file changed

Lines changed: 74 additions & 81 deletions

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‎src/ubic/basecode/ontology/model/OntologyTermImpl.java‎

Lines changed: 74 additions & 81 deletions
Original file line numberDiff line numberDiff line change
@@ -14,28 +14,16 @@
1414
*/
1515
package ubic.basecode.ontology.model;
1616

17+
import com.hp.hpl.jena.ontology.*;
18+
import com.hp.hpl.jena.rdf.model.*;
19+
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
20+
import org.apache.commons.collections4.CollectionUtils;
21+
1722
import java.util.Collection;
1823
import java.util.HashSet;
24+
import java.util.Objects;
1925
import java.util.Set;
2026

21-
import org.apache.commons.lang3.ObjectUtils;
22-
23-
import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
24-
import com.hp.hpl.jena.ontology.ConversionException;
25-
import com.hp.hpl.jena.ontology.Individual;
26-
import com.hp.hpl.jena.ontology.OntClass;
27-
import com.hp.hpl.jena.ontology.OntProperty;
28-
import com.hp.hpl.jena.ontology.OntResource;
29-
import com.hp.hpl.jena.ontology.Restriction;
30-
import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
31-
import com.hp.hpl.jena.rdf.model.Property;
32-
import com.hp.hpl.jena.rdf.model.RDFNode;
33-
import com.hp.hpl.jena.rdf.model.Resource;
34-
import com.hp.hpl.jena.rdf.model.ResourceFactory;
35-
import com.hp.hpl.jena.rdf.model.Statement;
36-
import com.hp.hpl.jena.rdf.model.StmtIterator;
37-
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
38-
3927
/**
4028
* Represents a class in an ontology
4129
*
@@ -45,30 +33,43 @@ public class OntologyTermImpl extends AbstractOntologyResource implements Ontolo
4533

4634
private static final String HAS_ALTERNATE_ID = "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId";
4735
private static final String NOTHING = "http://www.w3.org/2002/07/owl#Nothing";
48-
private static Set<String> REJECT_PARENT_URI = new HashSet<>();
4936

5037
/**
51-
*
38+
* Properties through which propagation is allowed for {@link #getChildren(boolean)}
5239
*/
53-
private static final long serialVersionUID = 1L;
40+
private static final Set<String> PROPAGATE_FROM_URIS = new HashSet<>();
5441

5542
/**
56-
* Should has_proper_part be used to indicate additional parent/child relations.
43+
* Properties through which propagation is allowed for {@link #getParents(boolean)}
44+
*/
45+
private static final Set<String> PROPAGATE_INTO_URIS = new HashSet<>();
46+
47+
private static final Set<String> REJECT_PARENT_URIS = new HashSet<>();
48+
49+
/**
50+
*
5751
*/
58-
private static final boolean USE_PROPER_PART_RESTRICTIONS = true;
52+
private static final long serialVersionUID = 1L;
53+
5954
static {
60-
REJECT_PARENT_URI.add( "http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant" );
61-
REJECT_PARENT_URI.add( "http://www.ifomis.org/bfo/1.1/snap#Continuant" );
62-
REJECT_PARENT_URI.add( "http://www.ifomis.org/bfo/1.1/snap#MaterialEntity" );
55+
CollectionUtils.addAll( PROPAGATE_INTO_URIS,
56+
"http://www.obofoundry.org/ro/ro.owl#proper_part_of",
57+
"http://purl.obolibrary.org/obo/BFO_0000050" );
58+
CollectionUtils.addAll( PROPAGATE_FROM_URIS,
59+
"http://www.obofoundry.org/ro/ro.owl#has_proper_part",
60+
"http://purl.obolibrary.org/obo/BFO_0000051" );
61+
REJECT_PARENT_URIS.add( "http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant" );
62+
REJECT_PARENT_URIS.add( "http://www.ifomis.org/bfo/1.1/snap#Continuant" );
63+
REJECT_PARENT_URIS.add( "http://www.ifomis.org/bfo/1.1/snap#MaterialEntity" );
6364

6465
// anatomical entity
65-
REJECT_PARENT_URI.add( "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_6" );
66+
REJECT_PARENT_URIS.add( "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_6" );
6667
}
6768

6869
private String label = null;
6970
private String localName = null;
7071

71-
private transient OntClass ontResource = null;
72+
private final transient OntClass ontResource;
7273

7374
public OntologyTermImpl( OntClass resource ) {
7475
this.ontResource = resource;
@@ -88,17 +89,18 @@ public boolean equals( Object obj ) {
8889

8990
final OntologyTermImpl that = ( OntologyTermImpl ) obj;
9091
if ( this.getUri() != null ) {
91-
return ObjectUtils.equals( this.getUri(), that.getUri() );
92+
return Objects.equals( this.getUri(), that.getUri() );
9293
}
93-
return ObjectUtils.equals( this.getTerm(), that.getTerm() );
94+
return Objects.equals( this.getTerm(), that.getTerm() );
9495
}
9596

9697
@Override
9798
public Collection<String> getAlternativeIds() {
9899
Collection<String> results = new HashSet<>();
99100

100101
Property alternate = ResourceFactory.createProperty( HAS_ALTERNATE_ID );
101-
for ( StmtIterator it = this.ontResource.listProperties( alternate ); it.hasNext(); ) {
102+
StmtIterator it = this.ontResource.listProperties( alternate );
103+
while ( it.hasNext() ) {
102104
Statement statement = it.next();
103105
results.add( statement.asTriple().getMatchObject().getLiteralLexicalForm() );
104106
}
@@ -152,10 +154,6 @@ public Collection<OntologyIndividual> getIndividuals() {
152154
return getIndividuals( true );
153155
}
154156

155-
/**
156-
* @param direct
157-
* @return
158-
*/
159157
@Override
160158
public Collection<OntologyIndividual> getIndividuals( boolean direct ) {
161159
Collection<OntologyIndividual> inds = new HashSet<>();
@@ -201,14 +199,12 @@ public Collection<OntologyRestriction> getRestrictions() {
201199
ExtendedIterator<OntClass> iterator = ontResource.listSuperClasses( false );
202200
while ( iterator.hasNext() ) {
203201
OntClass c = iterator.next();
204-
Restriction r = null;
202+
Restriction r;
205203
try {
206-
r = c.asRestriction();
207-
result.add( RestrictionFactory.asRestriction( r ) );
204+
result.add( RestrictionFactory.asRestriction( c.asRestriction() ) );
208205
} catch ( Exception e ) {
209206

210207
}
211-
212208
}
213209

214210
// Check superclasses for any ADDITIONAL restrictions.
@@ -221,9 +217,10 @@ public Collection<OntologyRestriction> getRestrictions() {
221217
} catch ( Exception e ) {
222218
// not a restriction, but a superclass that might have restrictions
223219
ExtendedIterator<OntClass> supClassesIt = c.listSuperClasses( false );
224-
loop: while ( supClassesIt.hasNext() ) {
220+
loop:
221+
while ( supClassesIt.hasNext() ) {
225222
OntClass sc = supClassesIt.next();
226-
Restriction sr = null;
223+
Restriction sr;
227224
try {
228225
sr = sc.asRestriction();
229226

@@ -253,7 +250,7 @@ public Collection<OntologyRestriction> getRestrictions() {
253250
*/
254251
@Override
255252
public String getTerm() {
256-
String res = null;
253+
String res;
257254
if ( this.label != null ) {
258255
res = this.label;
259256
} else if ( this.localName != null ) {
@@ -322,11 +319,11 @@ public boolean isTermObsolete() {
322319

323320
if ( parentOntologyTerm.getUri() != null
324321
&& parentOntologyTerm.getUri().equalsIgnoreCase(
325-
"http://bioontology.org/projects/ontologies/birnlex#_birnlex_retired_class" )
322+
"http://bioontology.org/projects/ontologies/birnlex#_birnlex_retired_class" )
326323
|| parentOntologyTerm
327-
.getUri()
328-
.equalsIgnoreCase(
329-
"http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#_birnlex_retired_class" ) ) {
324+
.getUri()
325+
.equalsIgnoreCase(
326+
"http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#_birnlex_retired_class" ) ) {
330327
return true;
331328
}
332329
}
@@ -389,13 +386,13 @@ private void getChildren( boolean direct, Collection<OntologyTerm> work ) {
389386
// some reasoners will infer owl#Nothing as a subclass of everything
390387
if ( c.getURI() == null || c.getURI().equals( NOTHING ) ) continue;
391388

392-
if ( USE_PROPER_PART_RESTRICTIONS && c.isRestriction() ) {
389+
if ( c.isRestriction() ) {
393390

394391
Restriction restriction = c.asRestriction();
395392

396393
OntProperty onProperty = restriction.getOnProperty();
397394

398-
if ( !onProperty.getURI().equals( "http://www.obofoundry.org/ro/ro.owl#has_proper_part" ) ) {
395+
if ( !PROPAGATE_FROM_URIS.contains( onProperty.getURI() ) ) {
399396
continue;
400397
}
401398

@@ -417,41 +414,39 @@ private void getChildren( boolean direct, Collection<OntologyTerm> work ) {
417414
// log.info( c );
418415
}
419416

420-
if ( USE_PROPER_PART_RESTRICTIONS ) {
421-
ExtendedIterator<OntClass> sciterator = this.ontResource.listSuperClasses( true );
422-
while ( sciterator.hasNext() ) {
423-
OntClass c = sciterator.next();
424-
if ( !c.isRestriction() ) {
425-
continue;
426-
}
417+
ExtendedIterator<OntClass> sciterator = this.ontResource.listSuperClasses( true );
418+
while ( sciterator.hasNext() ) {
419+
OntClass c = sciterator.next();
420+
if ( !c.isRestriction() ) {
421+
continue;
422+
}
427423

428-
Restriction restriction = c.asRestriction();
424+
Restriction restriction = c.asRestriction();
429425

430-
try {
431-
OntProperty onProperty = restriction.getOnProperty();
432-
if ( !onProperty.getURI().equals( "http://www.obofoundry.org/ro/ro.owl#has_proper_part" ) ) {
433-
continue;
434-
}
435-
} catch ( ConversionException e ) {
426+
try {
427+
OntProperty onProperty = restriction.getOnProperty();
428+
if ( !PROPAGATE_FROM_URIS.contains( onProperty.getURI() ) ) {
436429
continue;
437430
}
431+
} catch ( ConversionException e ) {
432+
continue;
433+
}
438434

439-
Resource r = getRestrictionValue( restriction );
440-
if ( r == null ) continue;
441-
442-
// if ( !( r instanceof OntClass ) ) {
443-
// // means our owl file is incomplete, is in tests.
444-
// log.info( r );
445-
// continue;
446-
// }
435+
Resource r = getRestrictionValue( restriction );
436+
if ( r == null ) continue;
447437

448-
OntologyTerm child = fromOntClass( ( OntClass ) r );
449-
if ( !work.contains( child ) ) {
450-
work.add( child );
451-
if ( !direct ) ( ( OntologyTermImpl ) child ).getChildren( false, work );
452-
}
438+
// if ( !( r instanceof OntClass ) ) {
439+
// // means our owl file is incomplete, is in tests.
440+
// log.info( r );
441+
// continue;
442+
// }
453443

444+
OntologyTerm child = fromOntClass( ( OntClass ) r );
445+
if ( !work.contains( child ) ) {
446+
work.add( child );
447+
if ( !direct ) ( ( OntologyTermImpl ) child ).getChildren( false, work );
454448
}
449+
455450
}
456451
}
457452

@@ -472,28 +467,27 @@ private void getParents( boolean direct, Collection<OntologyTerm> work ) {
472467
try {
473468
OntClass c = iterator.next();
474469

475-
if ( USE_PROPER_PART_RESTRICTIONS && c.isRestriction() ) {
470+
if ( c.isRestriction() ) {
476471
Restriction restriction = c.asRestriction();
477472

478473
OntProperty onProperty = restriction.getOnProperty();
479474

480475
assert onProperty != null;
481476

482477
// We ignore this... hack.
483-
if ( !onProperty.getURI().equals( "http://www.obofoundry.org/ro/ro.owl#proper_part_of" ) ) {
478+
if ( !PROPAGATE_INTO_URIS.contains( onProperty.getURI() ) ) {
484479
continue;
485480
}
486481

487482
Resource r = getRestrictionValue( restriction );
488483

489484
if ( r == null ) continue;
490485

491-
assert r != null;
492486
if ( log.isDebugEnabled() ) log.debug( " Some from:" + r + " " + onProperty.getURI() );
493487

494488
OntologyTerm parent = fromOntClass( ( OntClass ) r );
495489

496-
if ( REJECT_PARENT_URI.contains( parent.getUri() ) ) continue;
490+
if ( REJECT_PARENT_URIS.contains( parent.getUri() ) ) continue;
497491

498492
// avoid endless regression
499493
if ( !work.contains( parent ) ) {
@@ -505,7 +499,7 @@ private void getParents( boolean direct, Collection<OntologyTerm> work ) {
505499
// not a restriction.
506500
OntologyTerm parent = this.fromOntClass( c );
507501

508-
if ( REJECT_PARENT_URI.contains( parent.getUri() ) ) continue;
502+
if ( REJECT_PARENT_URIS.contains( parent.getUri() ) ) continue;
509503

510504
if ( !work.contains( parent ) ) {
511505
work.add( parent );
@@ -517,7 +511,6 @@ private void getParents( boolean direct, Collection<OntologyTerm> work ) {
517511
}
518512
} catch ( ConversionException e ) {
519513
if ( log.isDebugEnabled() ) log.debug( e.getMessage() );
520-
continue;
521514
}
522515

523516
}

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