unloadable: Problem parsing file:/home/hohndor/aberowl-meta/aberowl-server/onts/BIOMODELS_1.ont Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation. The following parsers were tried: 1) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@215527b8 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@7595fd83 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@4a36dfc4 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@23f62167 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d 12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 14) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@19079f96 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@437e3db0 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@1504106e 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@215527b8 Stack trace: org.xml.sax.SAXParseException; systemId: file:/home/hohndor/aberowl-meta/aberowl-server/onts/BIOMODELS_1.ont; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:78) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Content is not allowed in prolog. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@7595fd83 Stack trace: org.xml.sax.SAXParseException; systemId: file:/home/hohndor/aberowl-meta/aberowl-server/onts/BIOMODELS_1.ont; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Content is not allowed in prolog. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@4a36dfc4 Stack trace: Encountered " <PN_LOCAL> "PK\u0003\u0004\u0014\b\ufffd\ufffd\ufffd "" at line 1, column 1. Was expecting one of: "Ontology" ... "Prefix" ... (Line 0) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:79) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Encountered " <PN_LOCAL> "PK\u0003\u0004\u0014\b\ufffd\ufffd\ufffd "" at line 1, column 1. Was expecting one of: "Ontology" ... "Prefix" ... org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.generateParseException(OWLFunctionalSyntaxParser.java:3443) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.jj_consume_token(OWLFunctionalSyntaxParser.java:3363) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.Ontology(OWLFunctionalSyntaxParser.java:192) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.parse(OWLFunctionalSyntaxParser.java:171) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:77) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.RDFParseException: Expected ':', found '' [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Expected ':', found '' [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704) org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366) org.openrdf.rio.turtle.TurtleParser.verifyCharacterOrFail(TurtleParser.java:1190) org.openrdf.rio.turtle.TurtleParser.parseQNameOrBoolean(TurtleParser.java:1037) org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:617) org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448) org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382) org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260) org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@23f62167 Stack trace: Encountered 'PK���@�#+;�����biomodels-21.owlUT +{O{Oux ����]s�H�� �����>1W�C�}f�Lɲږ�-�zW�DB� �I�����%٢� se& |&�vW�|��������}�����$�F����_������n�vq��U������t:�ۯ�^Q4�F� �_'����[�?��U����۵7�����M���(��Ѵ���?���K�z6���8������m�W�GW���x'?��]G�&��k�Q���K.�b)?Y��Ϩ%?�>I�q���˶�?B�+?�짯�0���x����|p������/�ڋl5�_�_��3���Coy��5`O�aM�,c�֯��_W>��� �盿�~��R�:�k�~�yxx�k�J��f�A棩���h��˟�~�]�|��@?��[7C/�7�q����wL��l���[�F����M����ǟ^~Fg�[v�����w�����W�v{��l�\������ӟ��o޼Z�ۯ��g?�ϫ��(�z��,�J�x�����,�L~���͛���'���ҽC�//��h4>�u��`t9���Ӽ��Mr_�؛�y=��>�F���$��ht�ʲ�gG�{��l4��Z�xnjO�z�~�p��7��?�G���� FA������=�ͯ����K�˫�87��7{�{����P���$��}??�_�@땽0�cF�j_�Wɿ' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:102) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.RDFParseException: Expected '<' or '_', found: P [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Expected '<' or '_', found: P [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704) org.openrdf.rio.ntriples.NTriplesParser.reportFatalError(NTriplesParser.java:648) org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:348) org.openrdf.rio.nquads.NQuadsParser.parseQuad(NQuadsParser.java:123) org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:102) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.RDFParseException: Expected '<' or '_', found: P [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Expected '<' or '_', found: P [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704) org.openrdf.rio.ntriples.NTriplesParser.reportFatalError(NTriplesParser.java:648) org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:348) org.openrdf.rio.ntriples.NTriplesParser.parseTriple(NTriplesParser.java:280) org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:191) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.RDFParseException: Expected ':', found '' [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Expected ':', found '' [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704) org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366) org.openrdf.rio.turtle.TurtleParser.verifyCharacterOrFail(TurtleParser.java:1190) org.openrdf.rio.turtle.TurtleParser.parseQNameOrBoolean(TurtleParser.java:1037) org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:617) org.openrdf.rio.trig.TriGParser.parseGraph(TriGParser.java:132) org.openrdf.rio.trig.TriGParser.parseStatement(TriGParser.java:119) org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.RDFParseException: Found IOException during parsing [line 1, column 11] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Found IOException during parsing [line 1, column 11] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704) org.openrdf.rio.rdfjson.RDFJSONParser.reportFatalError(RDFJSONParser.java:155) org.openrdf.rio.rdfjson.RDFJSONParser.parse(RDFJSONParser.java:179) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.RDFParseException: File does not contain a binary RDF document org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) File does not contain a binary RDF document org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441) org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:424) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:693) org.openrdf.rio.binary.BinaryRDFParser.parse(BinaryRDFParser.java:87) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:252) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.RDFParseException: Could not parse JSONLD org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Could not parse JSONLD com.github.jsonldjava.sesame.SesameJSONLDParser.parse(SesameJSONLDParser.java:92) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) Unrecognized token 'PK': was expecting ('true', 'false' or 'null') at [Source: java.io.BufferedReader@53441214; line: 1, column: 11] com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1487) com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:518) com.fasterxml.jackson.core.json.ReaderBasedJsonParser._reportInvalidToken(ReaderBasedJsonParser.java:2300) com.fasterxml.jackson.core.json.ReaderBasedJsonParser._handleOddValue(ReaderBasedJsonParser.java:1459) com.fasterxml.jackson.core.json.ReaderBasedJsonParser.nextToken(ReaderBasedJsonParser.java:683) com.github.jsonldjava.utils.JsonUtils.fromReader(JsonUtils.java:107) com.github.jsonldjava.sesame.SesameJSONLDParser.parse(SesameJSONLDParser.java:88) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.RDFParseException: Content is not allowed in prolog. [line 1, column 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Content is not allowed in prolog. [line 1, column 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704) org.openrdf.rio.rdfxml.RDFXMLParser.reportFatalError(RDFXMLParser.java:1286) org.openrdf.rio.rdfxml.RDFXMLParser.fatalError(RDFXMLParser.java:1443) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.RDFParseException: Expected ':', found '' [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Expected ':', found '' [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704) org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366) org.openrdf.rio.turtle.TurtleParser.verifyCharacterOrFail(TurtleParser.java:1190) org.openrdf.rio.turtle.TurtleParser.parseQNameOrBoolean(TurtleParser.java:1037) org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:617) org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448) org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382) org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260) org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: Content is not allowed in prolog. [line 1, column 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Content is not allowed in prolog. [line 1, column 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.openrdf.rio.trix.TriXParser.parse(TriXParser.java:128) org.openrdf.rio.trix.TriXParser.parse(TriXParser.java:102) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) Content is not allowed in prolog. org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) info.aduna.xml.SimpleSAXParser.parse(SimpleSAXParser.java:226) info.aduna.xml.SimpleSAXParser.parse(SimpleSAXParser.java:213) org.openrdf.rio.trix.TriXParser.parse(TriXParser.java:121) org.openrdf.rio.trix.TriXParser.parse(TriXParser.java:102) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@19079f96 Stack trace: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 1. Was expecting one of: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:90) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Encountered "" at line 1, column 1. Was expecting one of: org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.generateParseException(TurtleParser.java:1960) org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.jj_consume_token(TurtleParser.java:1829) org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseDocument(TurtleParser.java:113) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:82) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@437e3db0 Stack trace: LINENO: 1 - expected newline or end of line but found: ??�_�@땽0�cF�j_�Wɿ LINE: PK���@�#+;�����biomodels-21.owlUT +{O{Oux ����]s�H�� �����>1W�C�}f�Lɲږ�-�zW�DB� �I�����%٢� se& |&�vW�|��������}�����$�F����_������n�vq��U������t:�ۯ�^Q4�F� �_'����[�?��U����۵7�����M���(��Ѵ���?���K�z6���8������m�W�GW���x'?��]G�&��k�Q���K.�b)?Y��Ϩ%?�>I�q���˶�?B�+?�짯�0���x����|p������/�ڋl5�_�_��3���Coy��5`O�aM�,c�֯��_W>��� �盿�~��R�:�k�~�yxx�k�J��f�A棩���h��˟�~�]�|��@?��[7C/�7�q����wL��l���[�F����M����ǟ^~Fg�[v�����w�����W�v{��l�\������ӟ��o޼Z�ۯ��g?�ϫ��(�z��,�J�x�����,�L~���͛���'���ҽC�//��h4>�u��`t9���Ӽ��Mr_�؛�y=��>�F���$��ht�ʲ�gG�{��l4��Z�xnjO�z�~�p��7��?�G���� FA������=�ͯ����K�˫�87��7{�{����P���$��}??�_�@땽0�cF�j_�Wɿ org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) LINENO: 1 - expected newline or end of line but found: ??�_�@땽0�cF�j_�Wɿ LINE: PK���@�#+;�����biomodels-21.owlUT +{O{Oux ����]s�H�� �����>1W�C�}f�Lɲږ�-�zW�DB� �I�����%٢� se& |&�vW�|��������}�����$�F����_������n�vq��U������t:�ۯ�^Q4�F� �_'����[�?��U����۵7�����M���(��Ѵ���?���K�z6���8������m�W�GW���x'?��]G�&��k�Q���K.�b)?Y��Ϩ%?�>I�q���˶�?B�+?�짯�0���x����|p������/�ڋl5�_�_��3���Coy��5`O�aM�,c�֯��_W>��� �盿�~��R�:�k�~�yxx�k�J��f�A棩���h��˟�~�]�|��@?��[7C/�7�q����wL��l���[�F����M����ǟ^~Fg�[v�����w�����W�v{��l�\������ӟ��o޼Z�ۯ��g?�ϫ��(�z��,�J�x�����,�L~���͛���'���ҽC�//��h4>�u��`t9���Ӽ��Mr_�؛�y=��>�F���$��ht�ʲ�gG�{��l4��Z�xnjO�z�~�p��7��?�G���� FA������=�ͯ����K�˫�87��7{�{����P���$��}??�_�@땽0�cF�j_�Wɿ org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.forceParseNlOrEof(OBOFormatParser.java:1339) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:523) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderFrame(OBOFormatParser.java:504) org.obolibrary.oboformat.parser.OBOFormatParser.parseOBODoc(OBOFormatParser.java:377) org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:335) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:79) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:58) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@1504106e Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " <NAME> "PK "" at line 1, column 1. Was expecting: <EOF> org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) Encountered " <NAME> "PK "" at line 1, column 1. Was expecting: <EOF> org.semanticweb.owlapi.krss2.parser.KRSS2Parser.generateParseException(KRSS2Parser.java:3187) org.semanticweb.owlapi.krss2.parser.KRSS2Parser.jj_consume_token(KRSS2Parser.java:3040) org.semanticweb.owlapi.krss2.parser.KRSS2Parser.parse(KRSS2Parser.java:141) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:270) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.RDFParseException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:111) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1017) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:973) org.semanticweb.owlapi.model.OWLOntologyManager$loadOntologyFromOntologyDocument.call(Unknown Source) src.RequestManager$_loadOntologies_closure11$_closure44.doCall(RequestManager.groovy:693) sun.reflect.GeneratedMethodAccessor89.invoke(Unknown Source) org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semarglproject.rdf.rdfa.RdfaParser.processException(RdfaParser.java:1130) org.semarglproject.source.XmlSource.process(XmlSource.java:50) org.semarglproject.source.StreamProcessor.processInternal(StreamProcessor.java:87) org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:167) org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:154) org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:109) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061) Content is not allowed in prolog. org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) org.semarglproject.source.XmlSource.process(XmlSource.java:48) org.semarglproject.source.StreamProcessor.processInternal(StreamProcessor.java:87) org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:167) org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:154) org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:109) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:250) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:193) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1061)

BIOMODELS - BioModels Ontology

OWL Representation of the models in the BioModels repository.

Ontology metadata

Homepage https://code.google.com/p/sbmlharvester/
Contactrobert.hoehndorf@kaust.edu.sa
Topicsmolecular modelling, computational biology, computational chemistry, biochemistry
SpeciesAll life
Class Count
Unsatisfiable classes
Date Download
Thu, 01 Mar 2012 00:00:00 GMT Download...

Query
OWL ClassOntologyLabelDefinition

Query
TitleAbstract

Query
LabelDescriptionDatasetDatatype(s)

See examples...

Use OBO-style URIs:

SPARQL Endpoint URI:

Versions

Properties