Error related to XML Parsing

[noorbakerally]

I am getting an error when creating the reasoner. It seems to be related with XML parsing. The codes being used and the errors:

Codes

String path = "http://elite.polito.it/ontologies/dogont.owl";
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLOntology ontology = manager.loadOntology(
                IRI.create(path));

        OWLlinkReasonerConfigurationImpl reasonerConfiguration = new OWLlinkReasonerConfigurationImpl();
        final OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
        final OWLReasoner reasoner = factory.createReasoner(ontology, reasonerConfiguration);

Error

/opt/java/bin/java -javaagent:/home/noor/Documents/apps/idea/lib/idea_rt.jar=36367:/home/noor/Documents/apps/idea/bin -Dfile.encoding=UTF-8 -classpath /opt/java/jre/lib/charsets.jar:/opt/java/jre/lib/deploy.jar:/opt/java/jre/lib/ext/cldrdata.jar:/opt/java/jre/lib/ext/dnsns.jar:/opt/java/jre/lib/ext/jaccess.jar:/opt/java/jre/lib/ext/jfxrt.jar:/opt/java/jre/lib/ext/localedata.jar:/opt/java/jre/lib/ext/nashorn.jar:/opt/java/jre/lib/ext/sunec.jar:/opt/java/jre/lib/ext/sunjce_provider.jar:/opt/java/jre/lib/ext/sunpkcs11.jar:/opt/java/jre/lib/ext/zipfs.jar:/opt/java/jre/lib/javaws.jar:/opt/java/jre/lib/jce.jar:/opt/java/jre/lib/jfr.jar:/opt/java/jre/lib/jfxswt.jar:/opt/java/jre/lib/jsse.jar:/opt/java/jre/lib/management-agent.jar:/opt/java/jre/lib/plugin.jar:/opt/java/jre/lib/resources.jar:/opt/java/jre/lib/rt.jar:/home/noor/IdeaProjects/RDFInjectionAndAlignment/target/classes:/home/noor/.m2/repository/org/neo4j/neo4j-enterprise/3.4.13/neo4j-enterprise-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j/3.4.13/neo4j-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-kernel/3.4.13/neo4j-kernel-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-graphdb-api/3.4.13/neo4j-graphdb-api-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-resource/3.4.13/neo4j-resource-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-procedure-api/3.4.13/neo4j-procedure-api-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-kernel-api/3.4.13/neo4j-kernel-api-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-common/3.4.13/neo4j-common-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-collections/3.4.13/neo4j-collections-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-primitive-collections/3.4.13/neo4j-primitive-collections-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-unsafe/3.4.13/neo4j-unsafe-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-io/3.4.13/neo4j-io-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-csv/3.4.13/neo4j-csv-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-logging/3.4.13/neo4j-logging-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-lucene-upgrade/3.4.13/neo4j-lucene-upgrade-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-configuration/3.4.13/neo4j-configuration-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-index/3.4.13/neo4j-index-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-spatial-index/3.4.13/neo4j-spatial-index-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-lucene-index/3.4.13/neo4j-lucene-index-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-graph-algo/3.4.13/neo4j-graph-algo-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-udc/3.4.13/neo4j-udc-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher/3.4.13/neo4j-cypher-3.4.13.jar:/home/noor/.m2/repository/org/scala-lang/scala-library/2.11.12/scala-library-2.11.12.jar:/home/noor/.m2/repository/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar:/home/noor/.m2/repository/org/neo4j/neo4j-graph-matching/3.1.9/neo4j-graph-matching-3.1.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-codegen/3.4.13/neo4j-codegen-3.4.13.jar:/home/noor/.m2/repository/org/ow2/asm/asm-util/6.2/asm-util-6.2.jar:/home/noor/.m2/repository/org/ow2/asm/asm-analysis/6.2/asm-analysis-6.2.jar:/home/noor/.m2/repository/org/ow2/asm/asm-tree/6.2/asm-tree-6.2.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-compiler-2.3/2.3.12/neo4j-cypher-compiler-2.3-2.3.12.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-frontend-2.3/2.3.12/neo4j-cypher-frontend-2.3-2.3.12.jar:/home/noor/.m2/repository/com/googlecode/concurrentlinkedhashmap/concurrentlinkedhashmap-lru/1.4.2/concurrentlinkedhashmap-lru-1.4.2.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-compiler-3.1/3.1.9/neo4j-cypher-compiler-3.1-3.1.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-frontend-3.1/3.1.9/neo4j-cypher-frontend-3.1-3.1.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-compiler-3.3/3.3.9/neo4j-cypher-compiler-3.3-3.3.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-frontend-3.3/3.3.9/neo4j-cypher-frontend-3.3-3.3.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-ir-3.3/3.3.9/neo4j-cypher-ir-3.3-3.3.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-logical-plans-3.3/3.3.9/neo4j-cypher-logical-plans-3.3-3.3.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-util-3.4/3.4.13/neo4j-cypher-util-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-planner-3.4/3.4.13/neo4j-cypher-planner-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/openCypher-frontend-1/3.4.13/openCypher-frontend-1-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-expression-3.4/3.4.13/neo4j-cypher-expression-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-ir-3.4/3.4.13/neo4j-cypher-ir-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-logical-plans-3.4/3.4.13/neo4j-cypher-logical-plans-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-planner-spi-3.4/3.4.13/neo4j-cypher-planner-spi-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-runtime-util/3.4.13/neo4j-cypher-runtime-util-3.4.13.jar:/home/noor/.m2/repo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-hc/4.5.5/fluent-hc-4.5.5.jar:/home/noor/.m2/repository/org/apache/httpcomponents/httpcore-osgi/4.4.9/httpcore-osgi-4.4.9.jar:/home/noor/.m2/repository/org/apache/httpcomponents/httpcore-nio/4.4.9/httpcore-nio-4.4.9.jar:/home/noor/.m2/repository/com/github/vsonnier/hppcrt/0.7.5/hppcrt-0.7.5.jar:/home/noor/.m2/repository/com/google/guava/guava/22.0/guava-22.0.jar:/home/noor/.m2/repository/com/google/errorprone/error_prone_annotations/2.0.18/error_prone_annotations-2.0.18.jar:/home/noor/.m2/repository/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar:/home/noor/.m2/repository/org/codehaus/mojo/animal-sniffer-annotations/1.14/animal-sniffer-annotations-1.14.jar:/home/noor/.m2/repository/com/google/code/findbugs/jsr305/3.0.2/jsr305-3.0.2.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-apibinding/5.1.10/owlapi-apibinding-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-api/5.1.10/owlapi-api-5.1.10.jar:/home/noor/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-impl/5.1.10/owlapi-impl-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-parsers/5.1.10/owlapi-parsers-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-oboformat/5.1.10/owlapi-oboformat-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-tools/5.1.10/owlapi-tools-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-rio/5.1.10/owlapi-rio-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/org.semanticweb.hermit/1.4.3.517/org.semanticweb.hermit-1.4.3.517.jar:/home/noor/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar:/home/noor/.m2/repository/org/apache/ws/commons/axiom/axiom-api/1.2.14/axiom-api-1.2.14.jar:/home/noor/.m2/repository/org/apache/geronimo/specs/geronimo-activation_1.1_spec/1.1/geronimo-activation_1.1_spec-1.1.jar:/home/noor/.m2/repository/org/apache/geronimo/specs/geronimo-javamail_1.4_spec/1.7.1/geronimo-javamail_1.4_spec-1.7.1.jar:/home/noor/.m2/repository/jaxen/jaxen/1.1.4/jaxen-1.1.4.jar:/home/noor/.m2/repository/org/apache/geronimo/specs/geronimo-stax-api_1.0_spec/1.0.1/geronimo-stax-api_1.0_spec-1.0.1.jar:/home/noor/.m2/repository/org/apache/james/apache-mime4j-core/0.7.2/apache-mime4j-core-0.7.2.jar:/home/noor/.m2/repository/org/apache/ws/commons/axiom/axiom-c14n/1.2.14/axiom-c14n-1.2.14.jar:/home/noor/.m2/repository/org/apache/ws/commons/axiom/axiom-impl/1.2.14/axiom-impl-1.2.14.jar:/home/noor/.m2/repository/org/apache/ws/commons/axiom/axiom-dom/1.2.14/axiom-dom-1.2.14.jar:/home/noor/.m2/repository/dk/brics/automaton/automaton/1.11-8/automaton-1.11-8.jar:/home/noor/.m2/repository/gnu/getopt/java-getopt/1.0.13/java-getopt-1.0.13.jar:/home/noor/.m2/repository/net/sf/trove4j/trove4j/3.0.3/trove4j-3.0.3.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/jfact/1.0.0/jfact-1.0.0.jar:/home/noor/.m2/repository/commons-cli/commons-cli/1.4/commons-cli-1.4.jar:/home/noor/.m2/repository/fr/emse/ci/sparql-generate/2.0-SNAPSHOT/sparql-generate-2.0-SNAPSHOT.jar:/home/noor/.m2/repository/us/monoid/web/resty/0.3.2/resty-0.3.2.jar:/home/noor/.m2/repository/net/java/dev/javacc/javacc/4.1/javacc-4.1.jar:/home/noor/Documents/repositories/github/owllink-owlapi/owllinkapi/target/owllinkapi-2.0.0.jar:/home/noor/Documents/repositories/github/owllink-owlapi/owllinkhttpxml/target/owllinkhttpxml-2.0.0.jar:/home/noor/Documents/repositories/github/owllink-owlapi/owllinkimpl/target/owllinkimpl-2.0.0.jar:/home/noor/Documents/repositories/github/owllink-owlapi/owllinkprotege/target/owllinkprotege-2.0.0.jar:/home/noor/Documents/repositories/github/owllink-owlapi/owllinkserver/target/owllinkserver-2.0.0.jar examples.TestKon
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/noor/.m2/repository/org/slf4j/slf4j-nop/1.7.25/slf4j-nop-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/noor/.m2/repository/org/apache/logging/log4j/log4j-slf4j-impl/2.11.0/log4j-slf4j-impl-2.11.0.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/noor/.m2/repository/fr/emse/ci/sparql-generate/2.0-SNAPSHOT/sparql-generate-2.0-SNAPSHOT.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.helpers.NOPLoggerFactory]
Exception in thread "main" org.semanticweb.owlapi.owllink.builtin.response.OWLlinkErrorResponseException: An error has occurred while processing 'Tell-'http://Konclude.com/Ontologies/UnnamedOntologies/1/1565623137724/'-Knowledge-Base-OWL2-XML-Axioms Command',
Error process protocol:
{notice}, [::Konclude::Command::Command]:Finish processing 'Tell-'http://Konclude.com/Ontologies/UnnamedOntologies/1/1565623137724/'-Knowledge-Base-OWL2-XML-Axioms Command' with all sub commands. Command closed.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Finish processing 'Tell-'http://Konclude.com/Ontologies/UnnamedOntologies/1/1565623137724/'-Knowledge-Base-OWL2-XML-Axioms Command'.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Stop processing 'Tell-'http://Konclude.com/Ontologies/UnnamedOntologies/1/1565623137724/'-Knowledge-Base-OWL2-XML-Axioms Command'.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Start processing 'Tell-'http://Konclude.com/Ontologies/UnnamedOntologies/1/1565623137724/'-Knowledge-Base-OWL2-XML-Axioms Command'.
{error}, An error has occurred while processing 'Parse-OWL2-XML-Ontology Command',
Sub-Error process protocol:
{notice}, [::Konclude::Command::Command]:Finish processing 'Parse-OWL2-XML-Ontology Command' with all sub commands. Command closed.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Finish processing 'Parse-OWL2-XML-Ontology Command'.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Stop processing 'Parse-OWL2-XML-Ontology Command'.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Start processing 'Parse-OWL2-XML-Ontology Command'.

	at org.semanticweb.owlapi.owllink.parser.OWLlinkErrorResponseElementHandler.getOWLLinkObject(OWLlinkErrorResponseElementHandler.java:58)
	at org.semanticweb.owlapi.owllink.parser.OWLlinkErrorResponseElementHandler.getOWLLinkObject(OWLlinkErrorResponseElementHandler.java:49)
	at org.semanticweb.owlapi.owllink.parser.OWLlinkResponseMessageElementHandler.handleChild(OWLlinkResponseMessageElementHandler.java:96)
	at org.semanticweb.owlapi.owllink.parser.AbstractOWLlinkErrorHandler.endElement(AbstractOWLlinkErrorHandler.java:75)
	at org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:458)
	at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
	at org.apache.xerces.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
	at org.apache.xerces.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
	at org.apache.xerces.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
	at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
	at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
	at javax.xml.parsers.SAXParser.parse(SAXParser.java:195)
	at org.semanticweb.owlapi.owllink.HTTPSessionImpl.performRequests(HTTPSessionImpl.java:209)
	at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.performRequests(OWLlinkHTTPXMLReasoner.java:526)
	at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.performRequest(OWLlinkHTTPXMLReasoner.java:530)
	at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.performRequestOWLAPI(OWLlinkHTTPXMLReasoner.java:544)
	at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.<init>(OWLlinkHTTPXMLReasoner.java:92)
	at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasonerFactory.createReasoner(OWLlinkHTTPXMLReasonerFactory.java:80)
	at examples.TestKon.main(TestKon.java:26)

Process finished with exit code 1

[bill-baumgartner]

Hi,

I have run into this same error message using code similar to that of @noorbakerally while attempting to process some of the Open Biomedical Ontologies, e.g.

• http://purl.obolibrary.org/obo/hp.owl
• http://purl.obolibrary.org/obo/cl.owl
• http://purl.obolibrary.org/obo/bfo.owl

Any thoughts as to how one might get past this would be greatly appreciated. Thanks!

Best,
Bill

[ignazio1977]

These errors look XML related but are not. Konclude is rejecting annotation property declarations.

Stripping the ontology and its import closure to pass to Konclude only the logical axioms gets rid of the error:

public static void main(String[] args)
    throws OWLOntologyCreationException, OWLOntologyStorageException {
    String path = "http://elite.polito.it/ontologies/dogont.owl";
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLOntology ontology = logicalAxiomsOnly(path, manager);
    OWLlinkReasonerConfigurationImpl reasonerConfiguration =
        new OWLlinkReasonerConfigurationImpl();
    final OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
    final OWLReasoner reasoner = factory.createReasoner(ontology, reasonerConfiguration);
}

protected static OWLOntology logicalAxiomsOnly(String path, OWLOntologyManager manager)
    throws OWLOntologyCreationException {
    OWLOntology l = manager.loadOntology(IRI.create(path));
    return manager.createOntology(
        l.importsClosure().flatMap(OWLOntology::logicalAxioms).collect(Collectors.toSet()));
}