无法使用 NTriples (OWLAPI) 保存 ontology
Can't save the ontology with NTriples (OWLAPI)
我尝试使用 owlapi 将 ontology 保存为 NTriples 格式。
当我尝试保存 ontology:
时出现此错误
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 1
at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
at java.base/java.util.Objects.checkIndex(Objects.java:373)
at java.base/java.util.ArrayList.get(ArrayList.java:426)
at java.base/java.util.Collections$UnmodifiableList.get(Collections.java:1321)
at java.base/java.util.Collections$UnmodifiableList.get(Collections.java:1321)
at org.semanticweb.owlapi.rdf.model.AbstractTranslator.lambda$visit(AbstractTranslator.java:710)
at java.base/java.lang.Iterable.forEach(Iterable.java:75)
at org.semanticweb.owlapi.rdf.model.AbstractTranslator.visit(AbstractTranslator.java:709)
at org.semanticweb.owlapi.model.OWLSameIndividualAxiom.accept(OWLSameIndividualAxiom.java:51)
at org.semanticweb.owlapi.rdf.model.AbstractTranslator.translate(AbstractTranslator.java:288)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline.accept(ReferencePipeline.java:195)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1624)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
at org.semanticweb.owlapi.rdf.RDFRendererBase.createGraph(RDFRendererBase.java:484)
at org.semanticweb.owlapi.rdf.RDFRendererBase.createGraph(RDFRendererBase.java:471)
at org.semanticweb.owlapi.rdf.RDFRendererBase.lambda$renderEntities(RDFRendererBase.java:294)
at java.base/java.util.stream.ReferencePipeline.accept(ReferencePipeline.java:176)
at java.base/java.util.ArrayList$Itr.forEachRemaining(ArrayList.java:1002)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
at org.semanticweb.owlapi.rdf.RDFRendererBase.renderEntities(RDFRendererBase.java:295)
at org.semanticweb.owlapi.rdf.RDFRendererBase.renderInOntologySignatureEntities(RDFRendererBase.java:280)
at org.semanticweb.owlapi.rdf.RDFRendererBase.renderOntologyComponents(RDFRendererBase.java:263)
at org.semanticweb.owlapi.rdf.RDFRendererBase.render(RDFRendererBase.java:258)
at org.semanticweb.owlapi.rio.RioStorer.storeOntology(RioStorer.java:230)
at org.semanticweb.owlapi.util.AbstractOWLStorer.store(AbstractOWLStorer.java:85)
at org.semanticweb.owlapi.util.AbstractOWLStorer.storeOntology(AbstractOWLStorer.java:72)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1324)
at preprocess.PositiveInference.inferringSemanticsofEquality(PositiveInference.java:117)
at preprocess.PositiveInference.inferencing(PositiveInference.java:85)
at preprocess.PositiveInference.main(PositiveInference.java:65)
错误引用的代码是：
NTriplesDocumentFormat nTriplesFormat = new NTriplesDocumentFormat();
try {
ontologyManager.saveOntology(ontologyInferred, nTriplesFormat, IRI.create(file.toURI()));
} catch (OWLOntologyStorageException e) {
e.printStackTrace();
}
ontology:
SameIndividual(<http://www.example.com/individual/eq#PB> )
SameIndividual(<http://www.example.com/individual/eq#transY> )
SameIndividual(<http://www.example.com/individual/eq#symX> )
SameIndividual(<http://www.example.com/individual/eq#OC> )
SameIndividual(<http://www.example.com/individual/eq#transZ> )
SameIndividual(<http://www.example.com/individual/eq#SAA> )
SameIndividual(<http://www.example.com/individual/eq#transX> )
SameIndividual(<http://www.example.com/individual/eq#OAC> )
SameIndividual(<http://www.example.com/individual/eq#refO> )
SameIndividual(<http://www.example.com/individual/eq#refS> )
SameIndividual(<http://www.example.com/individual/eq#SA> )
SameIndividual(<http://www.example.com/individual/eq#PAB> )
SameIndividual(<http://www.example.com/individual/eq#transX> <http://www.example.com/individual/eq#transY> <http://www.example.com/individual/eq#transZ> )
SameIndividual(<http://www.example.com/individual/eq#symY> )
基于OWL2RL/RDF规则eq-ref
推理的自反sameAs公理结果
如果：T(?s, ?p, ?o) 那么：T(?s, owl:sameAs, ?s)
SameIndividual(http://www.example.com/individual/eq#PB )
推理代码：
result.add(dataFactory.getOWLSameIndividualAxiom(individual, individual));
我可以将 ontology 保存为 OWLXMLFormat，但由于我正在构建一个需要三元组形式的数据集。有什么解决方案可以将其保存为任何三元组形式吗？
其他格式已经尝试过但错误：
NTriplesDocumentFormat nTriplesFormat = new NTriplesDocumentFormat();
N3DocumentFormat n3Format = new N3DocumentFormat();
TrigDocumentFormat trigFormat = new TrigDocumentFormat();
TurtleDocumentFormat turtleFormat = new TurtleDocumentFormat();
RioTurtleDocumentFormat rioFormat = new RioTurtleDocumentFormat();
编辑：
完整的推理代码：
public class InferredSameIndividualAxiomGenerator extends InferredIndividualAxiomGenerator<OWLSameIndividualAxiom>{
@Override
protected void addAxioms(OWLNamedIndividual entity, OWLReasoner reasoner, OWLDataFactory dataFactory, Set<OWLSameIndividualAxiom> result) {
Set<OWLNamedIndividual> sameIndividuals = asUnorderedSet(reasoner.getSameIndividuals(entity).entities());
sameIndividuals.add(entity);
result.add(dataFactory.getOWLSameIndividualAxiom(entity, entity));
if (sameIndividuals.size() > 1)
result.add(dataFactory.getOWLSameIndividualAxiom(sameIndividuals));
}
@Override
public String getLabel() {
return "Same Individuals T(?x, owl:sameAs, ?y)";
}
}
异常是一个错误（请按照评论中的建议进行报告），但请注意，这些不是合法的 OWL 公理。语法和语义规范显示 sameAs 至少需要两个参数。
（考虑公理应该允许同义词个体的定义；一个参数仅提供没有新信息）
如果公理是由推断的公理生成器生成的，那么看起来该代码也有错误。
可以使用 ONT-API 作为解决方法。
由于 ONTAPI 是以 RDF 为中心的 OWLAPI 实现，因此任何 RDF 序列化都没有问题（默认情况下有 OWL[=22 的替代=] 格式与 Jena 替代品）。
但是，公理 SameIndividual(x, x) 仍然是非法的，要创建这样的构造需要切换到 RDF API.
示例：
OWLOntologyManager m = OntManagers.createManager();
OWLOntology ont = m.createOntology();
String i = "http://i";
OntModel g = ((Ontology) ont).asGraphModel();
g.createIndividual(i).addSameIndividual(g.createIndividual(i));
ont.saveOntology(new NTriplesDocumentFormat(), System.out);
输出：
<http://i> <http://www.w3.org/2002/07/owl#sameAs> <http://i> .
<http://i> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#NamedIndividual> .
_:B0ee0d3dfX2D1fe4X2D4489X2D9fc3X2De18bae6cfab4 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Ontology> .
我尝试使用 owlapi 将 ontology 保存为 NTriples 格式。 当我尝试保存 ontology:
时出现此错误Exception in thread "main" java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 1
at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
at java.base/java.util.Objects.checkIndex(Objects.java:373)
at java.base/java.util.ArrayList.get(ArrayList.java:426)
at java.base/java.util.Collections$UnmodifiableList.get(Collections.java:1321)
at java.base/java.util.Collections$UnmodifiableList.get(Collections.java:1321)
at org.semanticweb.owlapi.rdf.model.AbstractTranslator.lambda$visit(AbstractTranslator.java:710)
at java.base/java.lang.Iterable.forEach(Iterable.java:75)
at org.semanticweb.owlapi.rdf.model.AbstractTranslator.visit(AbstractTranslator.java:709)
at org.semanticweb.owlapi.model.OWLSameIndividualAxiom.accept(OWLSameIndividualAxiom.java:51)
at org.semanticweb.owlapi.rdf.model.AbstractTranslator.translate(AbstractTranslator.java:288)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline.accept(ReferencePipeline.java:195)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1624)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
at org.semanticweb.owlapi.rdf.RDFRendererBase.createGraph(RDFRendererBase.java:484)
at org.semanticweb.owlapi.rdf.RDFRendererBase.createGraph(RDFRendererBase.java:471)
at org.semanticweb.owlapi.rdf.RDFRendererBase.lambda$renderEntities(RDFRendererBase.java:294)
at java.base/java.util.stream.ReferencePipeline.accept(ReferencePipeline.java:176)
at java.base/java.util.ArrayList$Itr.forEachRemaining(ArrayList.java:1002)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
at org.semanticweb.owlapi.rdf.RDFRendererBase.renderEntities(RDFRendererBase.java:295)
at org.semanticweb.owlapi.rdf.RDFRendererBase.renderInOntologySignatureEntities(RDFRendererBase.java:280)
at org.semanticweb.owlapi.rdf.RDFRendererBase.renderOntologyComponents(RDFRendererBase.java:263)
at org.semanticweb.owlapi.rdf.RDFRendererBase.render(RDFRendererBase.java:258)
at org.semanticweb.owlapi.rio.RioStorer.storeOntology(RioStorer.java:230)
at org.semanticweb.owlapi.util.AbstractOWLStorer.store(AbstractOWLStorer.java:85)
at org.semanticweb.owlapi.util.AbstractOWLStorer.storeOntology(AbstractOWLStorer.java:72)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1324)
at preprocess.PositiveInference.inferringSemanticsofEquality(PositiveInference.java:117)
at preprocess.PositiveInference.inferencing(PositiveInference.java:85)
at preprocess.PositiveInference.main(PositiveInference.java:65)
错误引用的代码是：
NTriplesDocumentFormat nTriplesFormat = new NTriplesDocumentFormat();
try {
ontologyManager.saveOntology(ontologyInferred, nTriplesFormat, IRI.create(file.toURI()));
} catch (OWLOntologyStorageException e) {
e.printStackTrace();
}
ontology:
SameIndividual(<http://www.example.com/individual/eq#PB> )
SameIndividual(<http://www.example.com/individual/eq#transY> )
SameIndividual(<http://www.example.com/individual/eq#symX> )
SameIndividual(<http://www.example.com/individual/eq#OC> )
SameIndividual(<http://www.example.com/individual/eq#transZ> )
SameIndividual(<http://www.example.com/individual/eq#SAA> )
SameIndividual(<http://www.example.com/individual/eq#transX> )
SameIndividual(<http://www.example.com/individual/eq#OAC> )
SameIndividual(<http://www.example.com/individual/eq#refO> )
SameIndividual(<http://www.example.com/individual/eq#refS> )
SameIndividual(<http://www.example.com/individual/eq#SA> )
SameIndividual(<http://www.example.com/individual/eq#PAB> )
SameIndividual(<http://www.example.com/individual/eq#transX> <http://www.example.com/individual/eq#transY> <http://www.example.com/individual/eq#transZ> )
SameIndividual(<http://www.example.com/individual/eq#symY> )
基于OWL2RL/RDF规则eq-ref
推理的自反sameAs公理结果如果：T(?s, ?p, ?o) 那么：T(?s, owl:sameAs, ?s)
SameIndividual(http://www.example.com/individual/eq#PB )
推理代码：
result.add(dataFactory.getOWLSameIndividualAxiom(individual, individual));
我可以将 ontology 保存为 OWLXMLFormat，但由于我正在构建一个需要三元组形式的数据集。有什么解决方案可以将其保存为任何三元组形式吗？
其他格式已经尝试过但错误：
NTriplesDocumentFormat nTriplesFormat = new NTriplesDocumentFormat();
N3DocumentFormat n3Format = new N3DocumentFormat();
TrigDocumentFormat trigFormat = new TrigDocumentFormat();
TurtleDocumentFormat turtleFormat = new TurtleDocumentFormat();
RioTurtleDocumentFormat rioFormat = new RioTurtleDocumentFormat();
编辑：
完整的推理代码：
public class InferredSameIndividualAxiomGenerator extends InferredIndividualAxiomGenerator<OWLSameIndividualAxiom>{
@Override
protected void addAxioms(OWLNamedIndividual entity, OWLReasoner reasoner, OWLDataFactory dataFactory, Set<OWLSameIndividualAxiom> result) {
Set<OWLNamedIndividual> sameIndividuals = asUnorderedSet(reasoner.getSameIndividuals(entity).entities());
sameIndividuals.add(entity);
result.add(dataFactory.getOWLSameIndividualAxiom(entity, entity));
if (sameIndividuals.size() > 1)
result.add(dataFactory.getOWLSameIndividualAxiom(sameIndividuals));
}
@Override
public String getLabel() {
return "Same Individuals T(?x, owl:sameAs, ?y)";
}
}
异常是一个错误（请按照评论中的建议进行报告），但请注意，这些不是合法的 OWL 公理。语法和语义规范显示 sameAs 至少需要两个参数。
（考虑公理应该允许同义词个体的定义；一个参数仅提供没有新信息）
如果公理是由推断的公理生成器生成的，那么看起来该代码也有错误。
可以使用 ONT-API 作为解决方法。
由于 ONTAPI 是以 RDF 为中心的 OWLAPI 实现，因此任何 RDF 序列化都没有问题（默认情况下有 OWL[=22 的替代=] 格式与 Jena 替代品）。
但是，公理 SameIndividual(x, x) 仍然是非法的，要创建这样的构造需要切换到 RDF API.
示例：
OWLOntologyManager m = OntManagers.createManager();
OWLOntology ont = m.createOntology();
String i = "http://i";
OntModel g = ((Ontology) ont).asGraphModel();
g.createIndividual(i).addSameIndividual(g.createIndividual(i));
ont.saveOntology(new NTriplesDocumentFormat(), System.out);
输出：
<http://i> <http://www.w3.org/2002/07/owl#sameAs> <http://i> .
<http://i> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#NamedIndividual> .
_:B0ee0d3dfX2D1fe4X2D4489X2D9fc3X2De18bae6cfab4 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Ontology> .