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ontopsychia.ontopsychia-social-module.1.orig? fall.myontoservicefull_falldetection.1.orig? neomark3.neomark-oral-cancer-ontology-version-3.2.orig? ecso.the-ecosystem-ontology.50.orig? dcmitype.dcmi-type-vocabulary.1.orig? neomark4.neomark-oral-cancer-ontology-version-4.1.orig? omit.ontology-for-microrna-target.40.orig? idobru.brucellosis-ontology.61.orig? ddi.ontology-for-drug-discovery-investigations.2.orig? tm-other-factors.traditional-medicine-other-factors-value-set.1.orig? ep.cardiac-electrophysiology-ontology.2.orig? eo.ethnicity-ontoloy.1.orig? cogpo.cognitive-paradigm-ontology.1.orig? sopharm.suggested-ontology-for-pharmacogenomics.18.orig? ncbitaxon.national-center-for-biotechnology-information-ncbi-organismal-classification.2.orig? sao.subcellular-anatomy-ontology.2.orig? rnprio.research-network-and-patient-registry-inventory-ontology.1.orig? apastatistical.apa-statistical-cluster.1.orig? repo.reproductive-trait-and-phenotype-ontology.3.orig? pathlex.anatomic-pathology-lexicon.5.orig? esso.epilepsy-syndrome-seizure-ontology.5.orig? inm-npi.interventionnelle-non-mdicamenteuse-inm.3.orig? onl-dp.dataset-processing.1.orig? hl7.health-level-seven-reference-implementation-model-version-3.3.orig? dinto.the-drug-drug-interactions-ontology.5.orig? dcm.dicom-controlled-terminology.9.orig? ogroup.orthologous-group-ontology.1.orig? dco.dispedia-core-ontology.34.orig? cao.clusters-of-orthologous-groups-cog-analysis-ontology.3.orig? phfumiado.phallusia-fumigata-anatomy-and-development-ontology.2.orig? adar.autism-dsm-adi-r-ontology.1.orig? vsao.vertebrate-skeletal-anatomy-ontology.20.orig? wb-ls.c-elegans-development-vocabulary.45.orig? oboe-sbc.santa-barbara-coastal-observation-ontology.1.orig? ontolurgences.emergency-care-ontology.1.orig? orth.orthology-ontology.4.orig? foodon.foodon.1.orig? dc.dublin-core.3.orig? cl.cell-ontology.61.orig? tao.teleost-anatomy-ontology.135.orig? cn.computer-network.1.orig? procchemical.chemical-process.1.orig? bt.biotop-ontology.12.orig? dco-debugit.debugit-core-ontology.1.orig? ecp.electronic-care-plan.2.orig? tads.tick-gross-anatomy-ontology.17.orig? phare.pharmacogenomic-relationships-ontology.2.orig? hiv.hiv-ontology.11.orig? ccont.cell-culture-ontology.3.orig? msv.metagenome-sample-vocabulary.1.orig? eco.evidence-and-conclusion-ontology.49.orig? birnlex.biomedical-informatics-research-network-project-lexicon.1.orig? natpro.natural-products-ontology.1.orig? mono.monogenean-ontology.2.orig? fb-sp.fly-taxonomy.7.orig? mso.multiple-sclerosis-ontology.2.orig? ecg.electrocardiography-ontology.12.orig? emap.mouse-gross-anatomy-and-development-ontology.7.orig? pseudo.pseudogene.1.orig? phmammado.phallusia-mammillata-anatomy-and-development-ontology.2.orig? piero.enzyme-reaction-ontology-for-annotating-partial-information-of-chemical-transformation.10.orig? edam-bioimaging.bioimaging-ontology.1.orig? pdon.parkinsons-disease-ontology.1.orig? dron.the-drug-ontology.6.orig? doid.human-disease-ontology.589.orig? gfo.general-formal-ontology.1.orig? lpt.livestock-product-trait-ontology.3.orig? heio.regional-healthcare-system-interoperability-and-information-exchange-measurement-ontology.17.orig? matrelement.material-element.1.orig? ocre.ontology-of-clinical-research.23.orig? rh-mesh.robert-hoehndorf-version-of-mesh.3.orig? ontovip.medical-image-simulation.1.orig? pxo.proteasix-ontology.10.orig? bp-metadata.bioportal-metadata-ontology.6.orig? pdo_cas.plant-diversity-ontology.1.orig? wb-phenotype.c-elegans-phenotype-vocabulary.240.orig? gro-cpga.cereal-plant-gross-anatomy-ontology.11.orig? moocciado.molgula-occidentalis-anatomy-and-development-ontology.2.orig? trak.taxonomy-for-rehabilitation-of-knee-conditions.5.orig? apadisorders.disorders-cluster.1.orig? caro.common-anatomy-reference-ontology.10.orig? hp.human-phenotype-ontology.563.orig? nmosp.neuromorphoorg-species-ontology.15.orig? ppio.protein-protein-interaction-ontology.23.orig? gene-cds.genomic-clinical-decision-support-ontology.1.orig? imgt-ontology.immunogenetics-ontology.4.orig? hrdo.disease-core-ontology-applied-to-rare-diseases.2.orig? pgxo.pgxo.1.orig? dideo.the-potential-drug-drug-interaction-and-potential-drug-drug-interaction-evidence-ontology.41.orig? matr.material.1.orig? ixno.interaction-ontology.2.orig? adalab.adalab-ontology.6.orig? comodi.comodi.5.orig? ontoma.ontology-of-alternative-medicine-french.1.orig? suicideo.suicideonto.1.orig? iso-annotations.iso-15926-2_2003_annotations.1.orig? dloro.dependency-layered-ontology-for-radiation-oncology.1.orig? hfo.heart-failure-ontology.1.orig? tgma.mosquito-gross-anatomy-ontology.17.orig? go.gene-ontology.1557.orig? tm-signs-and-sympts.traditional-medicine-signs-and-symptoms-value-set.1.orig? xeo.xeml-environment-ontology.4.orig? rctont.randomized-controlled-trials-ontology.1.orig? stato.statistics-ontology.11.orig? neumore.neural-motor-recovery-ontology.1.orig? dermo.human-dermatological-disease-ontology.10.orig? medeon.medical-error-ontology.1.orig? schema.schemaorg.1.orig? ontokbcf.ontological-knowledge-base-model-for-cystic-fibrosis.3.orig? gco.genome-component-ontology.3.orig? fao.fungal-gross-anatomy-ontology.20.orig? propreo.proteomics-data-and-process-provenance-ontology.2.orig? SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. java.io.IOException: Server returned HTTP response code: 403 for URL: http://data.bioontology.org/ontologies/ICNP/submissions/4/download at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1840) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at owl.cs.bioportal.download.BioPortalDownloadOntology.download(BioPortalDownloadOntology.java:148) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:81) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) java.lang.NullPointerException at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:2146) at org.apache.commons.io.IOUtils.copy(IOUtils.java:2102) at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:2123) at org.apache.commons.io.IOUtils.copy(IOUtils.java:2078) at org.apache.commons.io.FileUtils.copyToFile(FileUtils.java:1554) at org.apache.commons.io.FileUtils.copyInputStreamToFile(FileUtils.java:1528) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:82) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) PROCESSING: bim.biomedical-image-ontology.6.orig ... merge successful. PROCESSING: qibo.quantitative-imaging-biomarker-ontology.2.orig PROCESSING: doccc.diagnosis-ontology-of-clinical-care-classification.3.orig File /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv does not exist. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv File /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv does not exist. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: tma.tissue-microarray-ontology.1.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ancestro.ancestry-ontology.2.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: asdpto.autism-spectrum-disorder-phenotype-ontology.1.orig PROCESSING: flyglycodb.flyglycodb.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: sbol.synthetic-biology-open-language-visual-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ehda.human-developmental-anatomy-ontology-timed-version.6.orig PROCESSING: eol.environment-ontology-for-livestock.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. PROCESSING: oborel.open-biological-and-biomedical-ontologies-relationship-types.9.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: pdo.pathogenic-disease-ontology.6.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: nonrcto.non-randomized-controlled-trials-ontology.1.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: obi.ontology-for-biomedical-investigations.32.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: idqa.image-and-data-quality-assessment-ontology.8.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: Problem parsing http://www.owl-ontologies.com/assert.owl 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@220b35fe 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@72110b0 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@7cfe616f 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@50c319ea 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@5cde9fc1 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@5b3949ff 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@67f5c123 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@220b35fe Stack trace: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=2:column=280] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) [line=2:column=280] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.verify(RDFParser.java:451) org.semanticweb.owlapi.rdf.rdfxml.parser.StartRDF.startElement(StartRDF.java:187) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@72110b0 Stack trace: org.xml.sax.SAXParseException; systemId: http://www.owl-ontologies.com/assert.owl; lineNumber: 3; columnNumber: 544; The reference to entity "b" must end with the ';' delimiter. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) The reference to entity "b" must end with the ';' delimiter. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEntityReference(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@7cfe616f Stack trace: Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@50c319ea Stack trace: Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:102) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: The declaration for the entity "ContentType" must end with '>'. [line 81, column 5] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) The declaration for the entity "ContentType" must end with '>'. [line 81, column 5] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) The declaration for the entity "ContentType" must end with '>'. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLDTDScannerImpl.scanEntityDecl(Unknown Source) org.apache.xerces.impl.XMLDTDScannerImpl.scanDecls(Unknown Source) org.apache.xerces.impl.XMLDTDScannerImpl.scanDTDExternalSubset(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@5cde9fc1 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@5b3949ff Stack trace: LINENO: 3 - expected newline or end of line but found: catch(err){}}try{window.onload=handleABPDetect();}catch(err){}owl-ontologies.com LINE: owl-ontologies.com org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) LINENO: 3 - expected newline or end of line but found: catch(err){}}try{window.onload=handleABPDetect();}catch(err){}owl-ontologies.com LINE: owl-ontologies.com 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.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:58) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@67f5c123 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " ">" " "" at line 1, column 1. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://www.owl-ontologies.com/assert.owl 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@220b35fe 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@72110b0 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@7cfe616f 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@50c319ea 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@5cde9fc1 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@5b3949ff 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@67f5c123 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@220b35fe Stack trace: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=2:column=280] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) [line=2:column=280] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.verify(RDFParser.java:451) org.semanticweb.owlapi.rdf.rdfxml.parser.StartRDF.startElement(StartRDF.java:187) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@72110b0 Stack trace: org.xml.sax.SAXParseException; systemId: http://www.owl-ontologies.com/assert.owl; lineNumber: 3; columnNumber: 544; The reference to entity "b" must end with the ';' delimiter. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) The reference to entity "b" must end with the ';' delimiter. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEntityReference(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@7cfe616f Stack trace: Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@50c319ea Stack trace: Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:102) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: The declaration for the entity "ContentType" must end with '>'. [line 81, column 5] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) The declaration for the entity "ContentType" must end with '>'. [line 81, column 5] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) The declaration for the entity "ContentType" must end with '>'. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLDTDScannerImpl.scanEntityDecl(Unknown Source) org.apache.xerces.impl.XMLDTDScannerImpl.scanDecls(Unknown Source) org.apache.xerces.impl.XMLDTDScannerImpl.scanDTDExternalSubset(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@5cde9fc1 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@5b3949ff Stack trace: LINENO: 3 - expected newline or end of line but found: catch(err){}}try{window.onload=handleABPDetect();}catch(err){}owl-ontologies.com LINE: owl-ontologies.com org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) LINENO: 3 - expected newline or end of line but found: catch(err){}}try{window.onload=handleABPDetect();}catch(err){}owl-ontologies.com LINE: owl-ontologies.com 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.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:58) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@67f5c123 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " ">" " "" at line 1, column 1. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:234) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 31 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ogdi.ontology-for-genetic-disease-investigations.3.orig PROCESSING: admin.nurse-administrator.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: co-wheat.wheat-trait-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bhn.biologie-hors-nomenclature.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bho.bleeding-history-phenotype-ontology.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mccv.microbial-culture-collection-vocabulary.10.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: gro.gene-regulation-ontology.5.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: enm.enanomapper.14.orig PROCESSING: glyco.glycomics-ontology.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://www.obofoundry.org/ro/ro.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://www.obofoundry.org/ro/ro.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 31 more Caused by: java.io.FileNotFoundException: http://www.obofoundry.org/ro/ro.owl at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 36 more Caused by: java.io.FileNotFoundException: http://www.obofoundry.org/ro/ro.owl at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 39 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: tipssewatruk.sewatruk.3.orig org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/home/zeus/experiments/bpdownload/repo/tmp/tipssewatruk.sewatruk.3.orig 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@1958b234 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@53512b01 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@f44ea4d 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@53e3187b 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@77c1ad99 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@71354e6d 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@55aa88f0 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@1958b234 Stack trace: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=2:column=34] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [line=2:column=34] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.verify(RDFParser.java:451) org.semanticweb.owlapi.rdf.rdfxml.parser.StartRDF.startElement(StartRDF.java:187) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@53512b01 Stack trace: org.xml.sax.SAXParseException; systemId: file:/home/zeus/experiments/bpdownload/repo/tmp/tipssewatruk.sewatruk.3.orig; lineNumber: 17; columnNumber: 52; Attribute name "crossorigin" associated with an element type "link" must be followed by the ' = ' character. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Attribute name "crossorigin" associated with an element type "link" must be followed by the ' = ' character. 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.XMLNSDocumentScannerImpl.scanAttribute(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@f44ea4d Stack trace: Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@53e3187b Stack trace: Encountered '' 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: Attribute name "crossorigin" associated with an element type "link" must be followed by the ' = ' character. [line 17, column 52] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Attribute name "crossorigin" associated with an element type "link" must be followed by the ' = ' character. [line 17, column 52] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:96) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:89) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) Attribute name "crossorigin" associated with an element type "link" must be followed by the ' = ' character. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanAttribute(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@77c1ad99 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@71354e6d Stack trace: LINENO: 1 - Could not find tag separator ':' in line. LINE: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) LINENO: 1 - Could not find tag separator ':' in line. LINE: org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521) 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:197) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@55aa88f0 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Encountered " ">" " "" at line 1, column 1. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:234) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) PROCESSING: cedarpc.cedar-provisional-classes.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: onl-msa.mental-state-assessment.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mooccuado.molgula-occulta-anatomy-and-development-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. PROCESSING: pco.population-and-community-ontology.12.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ofsmr.open-food-safety-model-repository.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: sio.semanticscience-integrated-ontology.72.orig ... merge successful. PROCESSING: poro.porifera-ontology.8.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mccl.cell-line-ontology-by-mahadevan.2.orig ... merge successful. PROCESSING: oae.ontology-of-adverse-events.160.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mego.mobile-genetic-element-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: fdsajfahsjk.owl_xml_tool5.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://example.com/owl/families/import/familyImport2 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.owlxml.parser.OWLImportsHandler.endElement(PARSER_OWLXMLVocabulary.java:3004) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:422) at org.apache.xerces.parsers.AbstractSAXParser.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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:60) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://example.com/owl/families/import/familyImport2 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 24 more Caused by: java.io.FileNotFoundException: http://example.com/owl/families/import/familyImport2 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 29 more Caused by: java.io.FileNotFoundException: http://example.com/owl/families/import/familyImport2 at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 32 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: iso-15926-2_2003.iso-15926-2_2003_oil.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: Problem parsing http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl 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@70eefdec 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@2f9e7c8e 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@2818e50c 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@63a0fd8d 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@aae68c2 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@78233bb 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@52553e18 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@70eefdec Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:78) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. 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.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@2f9e7c8e Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@2818e50c Stack trace: Encountered " " "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " " "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@63a0fd8d Stack trace: Encountered ' ' at line 1 column 3. Expected either 'Ontology:' or 'Prefix:' (Line 1) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:102) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) White spaces are required after keyword PUBLIC in DOCTYPE decl. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@aae68c2 Stack trace: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@78233bb Stack trace: LINENO: 1 - Could not find tag separator ':' in line. LINE: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) LINENO: 1 - Could not find tag separator ':' in line. LINE: org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521) 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.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@52553e18 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 3. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " ">" " "" at line 1, column 3. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl 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@70eefdec 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@2f9e7c8e 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@2818e50c 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@63a0fd8d 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@aae68c2 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@78233bb 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@52553e18 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@70eefdec Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:78) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@2f9e7c8e Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. 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.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@2818e50c Stack trace: Encountered " " "" at line 1, column 3. Was expecting one of: "Ontology" ... "Prefix" ... (Line 0) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:79) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " " "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@63a0fd8d Stack trace: Encountered ' ' at line 1 column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) White spaces are required after keyword PUBLIC in DOCTYPE decl. 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.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@aae68c2 Stack trace: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 3. Was expecting one of: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:90) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@78233bb Stack trace: LINENO: 1 - Could not find tag separator ':' in line. LINE: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) LINENO: 1 - Could not find tag separator ':' in line. LINE: org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521) 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.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@52553e18 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 3. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " ">" " "" at line 1, column 3. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:234) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 32 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: aeo.anatomical-entity-ontology.6.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. PROCESSING: emo.enzyme-mechanism-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: icps.international-classification-for-patient-safety.7.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException: Ontology already exists. OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1065) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.man.ac.uk.experiment.util.ExperimentUtilities.getReferenceOntologyInDir(ExperimentUtilities.java:78) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:90) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI() VersionIRI()) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:728) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:561) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:589) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:678) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.applyChange(OWLRDFConsumer.java:663) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TypeOntologyHandler.handleTriple(TripleHandlers.java:2840) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:177) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElement.startElement(StartRDF.java:311) at org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.startElement(StartRDF.java:374) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ... 9 more ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: dikb.drug-interaction-knowledge-base-ontology.5.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: glycordf.glycordf.14.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://purl.org/mp/ at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://purl.org/mp/ at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 32 more Caused by: java.io.FileNotFoundException: http://purl.org/mp/ at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 37 more Caused by: java.io.FileNotFoundException: http://purl.org/mp/ at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 40 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: onl-mr-da.magnetic-resonance-dataset-acquisition-ontology.1.orig PROCESSING: vivo.vivo-ontology-for-researcher-discovery.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: phylont.phylogenetic-ontology.7.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: shr.student-health-record-ontology.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: adw.animal-natural-history-and-life-history-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mwla.medical-web-lifestyle-aggregator.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: cno_acronym.cno_name.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mirnao.microrna-ontology.11.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bfo.basic-formal-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ado.alzheimers-disease-ontology.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: triage.nurse-triage.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: brct.brain-region--cell-type-terminology.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://semanticweb.org/latitude_user/ontologies/2014/8/untitled-ontology-7 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.owlxml.parser.OWLImportsHandler.endElement(PARSER_OWLXMLVocabulary.java:3004) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:422) 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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:60) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://semanticweb.org/latitude_user/ontologies/2014/8/untitled-ontology-7 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 27 more Caused by: java.io.FileNotFoundException: http://semanticweb.org/latitude_user/ontologies/2014/8/untitled-ontology-7 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 32 more Caused by: java.io.FileNotFoundException: http://semanticweb.org/latitude_user/ontologies/2014/8/untitled-ontology-7 at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 35 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: geospecies.geospecies-ontology.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://rdf.geospecies.org/methods/observationMethod.rdf at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://rdf.geospecies.org/methods/observationMethod.rdf at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 32 more Caused by: java.io.FileNotFoundException: http://rdf.geospecies.org/methods/observationMethod.rdf at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 37 more Caused by: java.io.FileNotFoundException: http://rdf.geospecies.org/methods/observationMethod.rdf at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 40 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ehdaa.human-developmental-anatomy-ontology-abstract-version-1.6.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: chembio.systems-chemical-biology-and-chemogenomics-ontology.9.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: rex.physico-chemical-process.6.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: pav.pav-provenance-authoring-and-versioning.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: jerm.sysmo-jerm-ontology-of-systems-biology-for-micro-organisms.14.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: chd.congenital-heart-defects-ontology.5.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ntdo.neglected-tropical-disease-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: biomodels.biomodels-ontology.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: rexo.regulation-of-gene-expression-ontolology.6.orig PROCESSING: chmo.chemical-methods-ontology.18.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: pae.plant-anatomy.13.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: cptac.cptac-proteomics-pipeline-infrastructure-ontology.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: tdwgspec.tdwg-specimen-lsid-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: dmto.diabetes-mellitus-treatment-ontology.1.orig org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/home/zeus/experiments/bpdownload/repo/tmp/dmto.diabetes-mellitus-treatment-ontology.1.orig 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@30695c8b 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@43dee152 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@39a970a6 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@c51fbbc 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@e427a36 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@1fcdd03b 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@23ec4513 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@30695c8b Stack trace: org.xml.sax.SAXParseException; systemId: file:/home/zeus/experiments/bpdownload/repo/tmp/dmto.diabetes-mellitus-treatment-ontology.1.orig; 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) 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@43dee152 Stack trace: org.xml.sax.SAXParseException; systemId: file:/home/zeus/experiments/bpdownload/repo/tmp/dmto.diabetes-mellitus-treatment-ontology.1.orig; 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) 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@39a970a6 Stack trace: Encountered " "Rar!\u001a\u0007\u03d0s "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Encountered " "Rar!\u001a\u0007\u03d0s "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@c51fbbc Stack trace: Encountered 'Rar!?s' 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: Content is not allowed in prolog. [line 1, column 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Content is not allowed in prolog. [line 1, column 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:96) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:89) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) 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.rdf.turtle.parser.TurtleOntologyParser@e427a36 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@1fcdd03b Stack trace: LINENO: 1 - Could not find tag separator ':' in line. LINE: Rar!?s org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) LINENO: 1 - Could not find tag separator ':' in line. LINE: Rar!?s org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521) 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:197) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@23ec4513 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " "Rar "" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Encountered " "Rar "" at line 1, column 1. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:234) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) PROCESSING: gexo.gene-expression-ontology.2.orig PROCESSING: nigo.neural-immune-gene-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: taxrank.taxonomic-rank-vocabulary.9.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: haauraado.halocynthia-aurantium-anatomy-and-development-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: gfvo.genomic-feature-and-variation-ontology.20.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: aba-amb.allen-brain-atlas-aba-adult-mouse-brain-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: haroreado.halocynthia-roretzi-anatomy-and-development-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bp.biopax-ontology-of-biological-pathways.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: ogg-mm.ontology-of-genes-and-genomes---mouse.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: icd11-bodysystem.body-system-terms-from-icd11.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: cmpo.cellular-microscopy-phenotype-ontology.14.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: flu.influenza-ontology.27.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://www.obofoundry.org/ro/ro.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://www.obofoundry.org/ro/ro.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 58 more Caused by: java.io.FileNotFoundException: http://www.obofoundry.org/ro/ro.owl at sun.reflect.GeneratedConstructorAccessor96.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 63 more Caused by: java.io.FileNotFoundException: http://www.obofoundry.org/ro/ro.owl at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 66 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: iso19115roles.iso-19115-role-codes.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: matrcompound.material-compound.1.orig PROCESSING: reto.regulation-of-transcription-ontology.7.orig ... merge successful. ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bdo.bone-dysplasia-ontology.9.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: abd.anthology-of-biosurveillance-diseases.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: vhog.vertebrate-homologous-organ-group-ontology.11.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: sep.sample-processing-and-separation-techniques-ontology.3.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: Problem parsing http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo 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@b31f81e 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@75557791 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@71a0802d 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@d5ac1c5 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@2ddbc0d8 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@43dac92d 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@c947cee 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@b31f81e Stack trace: org.xml.sax.SAXParseException; systemId: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo; 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) 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@75557791 Stack trace: org.xml.sax.SAXParseException; systemId: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo; 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) 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@71a0802d Stack trace: Encountered " "format-version: "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) Encountered " "format-version: "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@d5ac1c5 Stack trace: Encountered 'format-version: 1.2' 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: Content is not allowed in prolog. [line 1, column 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) Content is not allowed in prolog. [line 1, column 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) 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.rdf.turtle.parser.TurtleOntologyParser@2ddbc0d8 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@43dac92d Stack trace: LINENO: 14 - expected newline or end of line but found: LINE: def: "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia "http://www.wikipedia.org/"] org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) LINENO: 14 - expected newline or end of line but found: LINE: def: "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia "http://www.wikipedia.org/"] org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.forceParseNlOrEof(OBOFormatParser.java:1339) org.obolibrary.oboformat.parser.OBOFormatParser.parseEOL(OBOFormatParser.java:1307) org.obolibrary.oboformat.parser.OBOFormatParser.parseTermFrameClauseEOL(OBOFormatParser.java:629) org.obolibrary.oboformat.parser.OBOFormatParser.parseTermFrame(OBOFormatParser.java:601) org.obolibrary.oboformat.parser.OBOFormatParser.parseEntityFrame(OBOFormatParser.java:566) org.obolibrary.oboformat.parser.OBOFormatParser.parseOBODoc(OBOFormatParser.java:381) org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:335) org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@c947cee Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " "format-version: "" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) Encountered " "format-version: "" at line 1, column 1. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) at org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) at org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) at org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:58) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo 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@b31f81e 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@75557791 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@71a0802d 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@d5ac1c5 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@2ddbc0d8 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@43dac92d 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@c947cee 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@b31f81e Stack trace: org.xml.sax.SAXParseException; systemId: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo; 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) 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@75557791 Stack trace: org.xml.sax.SAXParseException; systemId: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo; 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) 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@71a0802d Stack trace: Encountered " "format-version: "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) Encountered " "format-version: "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@d5ac1c5 Stack trace: Encountered 'format-version: 1.2' 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) 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.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) Content is not allowed in prolog. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$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.rdf.turtle.parser.TurtleOntologyParser@2ddbc0d8 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@43dac92d Stack trace: LINENO: 14 - expected newline or end of line but found: LINE: def: "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia "http://www.wikipedia.org/"] org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) LINENO: 14 - expected newline or end of line but found: LINE: def: "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia "http://www.wikipedia.org/"] org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.forceParseNlOrEof(OBOFormatParser.java:1339) org.obolibrary.oboformat.parser.OBOFormatParser.parseEOL(OBOFormatParser.java:1307) org.obolibrary.oboformat.parser.OBOFormatParser.parseTermFrameClauseEOL(OBOFormatParser.java:629) org.obolibrary.oboformat.parser.OBOFormatParser.parseTermFrame(OBOFormatParser.java:601) org.obolibrary.oboformat.parser.OBOFormatParser.parseEntityFrame(OBOFormatParser.java:566) org.obolibrary.oboformat.parser.OBOFormatParser.parseOBODoc(OBOFormatParser.java:381) org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:335) org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@c947cee Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " "format-version: "" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) Encountered " "format-version: "" at line 1, column 1. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:308) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:88) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:376) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:234) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 15 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ao.asthma-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: omrse.ontology-of-medically-related-social-entities.33.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: teddy.terminology-for-the-description-of-dynamics.11.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: apaneurocluster.apa-neuro-cluster.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: alexandergarcia.name at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.owlxml.parser.OWLImportsHandler.endElement(PARSER_OWLXMLVocabulary.java:3004) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:422) 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 org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:60) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: alexandergarcia.name at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 27 more Caused by: java.net.UnknownHostException: alexandergarcia.name at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:175) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1169) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1105) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:999) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:933) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:102) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 32 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: flopo.flora-phenotype-ontology.8.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bco.biological-collections-ontology.9.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: aao.amphibian-gross-anatomy-ontology.8.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: elig.eligibility-feature-hierarchy.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: medo.mouse-experimental-design-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: apatandt.apa-tests-and-testing-cluster.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: alexandergarcia.name at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.owlxml.parser.OWLImportsHandler.endElement(PARSER_OWLXMLVocabulary.java:3004) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:422) 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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:60) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: alexandergarcia.name at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 27 more Caused by: java.net.UnknownHostException: alexandergarcia.name at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:175) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1169) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1105) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:999) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:933) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:102) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 32 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: plio.protein-ligand-interaction-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: hom.ontology-of-homology-and-related-concepts-in-biology.6.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: gmm.gomapman.25.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: nifdys.neuroscience-information-framework-nif-dysfunction-ontlogy.14.orig PROCESSING: gmo.growth-medium-onotology.6.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: mimi.case.edu at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: mimi.case.edu at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 31 more Caused by: java.net.UnknownHostException: mimi.case.edu at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:175) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1169) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1105) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:999) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:933) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:102) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 36 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: pato.phenotypic-quality-ontology.164.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: sdo.sleep-domain-ontology.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: phage.phylogenetics-ontology.5.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: onstr.ontology-for-newborn-screening-follow-up-and-translational-research.5.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://onstr.googlecode.com/svn/tags/currentRelease/2014-09-03/ONSTR_Obsolete.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://onstr.googlecode.com/svn/tags/currentRelease/2014-09-03/ONSTR_Obsolete.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 32 more Caused by: java.io.FileNotFoundException: http://onstr.googlecode.com/svn/tags/currentRelease/2014-09-03/ONSTR_Obsolete.owl at sun.reflect.GeneratedConstructorAccessor96.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 37 more Caused by: java.io.FileNotFoundException: http://onstr.googlecode.com/svn/tags/currentRelease/2014-09-03/ONSTR_Obsolete.owl at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 40 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: hpio.host-pathogen-interactions-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ctont.epoch-clinical-trial-ontology.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: epoch.stanford.edu at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: epoch.stanford.edu at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 31 more Caused by: java.net.UnknownHostException: epoch.stanford.edu at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:175) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1169) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1105) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:999) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:933) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:102) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 36 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: cedarvs.cedar-value-sets.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: phenx.phenx-phenotypic-terms.16.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ontodt.ontology-of-datatypes.6.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ooevv.ontology-of-experimental-variables-and-values.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bsao.botryllus-schlosseri-anatomy-and-development-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: apaocuemploy.apa-occupational-and-employment-cluster.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: alexandergarcia.name at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.owlxml.parser.OWLImportsHandler.endElement(PARSER_OWLXMLVocabulary.java:3004) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:422) 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 org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:60) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: alexandergarcia.name at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 27 more Caused by: java.net.UnknownHostException: alexandergarcia.name at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:175) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1169) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1105) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:999) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:933) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:102) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 32 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: top-menelas.menelas-project-top-level-ontology.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: sd3.simulation-delivery-and-documentation-deviations.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ovae.ontology-of-vaccine-adverse-events.10.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: teo.time-event-ontology.4.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: Problem parsing http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl 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@4942c274 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@72b624dc 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@2db8099c 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@5ac290ef 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@61e43586 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@1fe9b6c1 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@2517e532 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@4942c274 Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:78) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. 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.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@72b624dc Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@2db8099c Stack trace: Encountered " " "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " " "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@5ac290ef Stack trace: Encountered ' ' at line 1 column 3. Expected either 'Ontology:' or 'Prefix:' (Line 1) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:102) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) White spaces are required after keyword PUBLIC in DOCTYPE decl. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@61e43586 Stack trace: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@1fe9b6c1 Stack trace: LINENO: 1 - Could not find tag separator ':' in line. LINE: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) LINENO: 1 - Could not find tag separator ':' in line. LINE: org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521) 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.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@2517e532 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 3. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " ">" " "" at line 1, column 3. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl 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@4942c274 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@72b624dc 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@2db8099c 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@5ac290ef 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@61e43586 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@1fe9b6c1 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@2517e532 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@4942c274 Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:78) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@72b624dc Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/lists/2008/09/11/list.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. 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.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@2db8099c Stack trace: Encountered " " "" at line 1, column 3. Was expecting one of: "Ontology" ... "Prefix" ... (Line 0) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:79) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " " "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@5ac290ef Stack trace: Encountered ' ' at line 1 column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) White spaces are required after keyword PUBLIC in DOCTYPE decl. 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.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@61e43586 Stack trace: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 3. Was expecting one of: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:90) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@1fe9b6c1 Stack trace: LINENO: 1 - Could not find tag separator ':' in line. LINE: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) LINENO: 1 - Could not find tag separator ':' in line. LINE: org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521) 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.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@2517e532 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 3. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " ">" " "" at line 1, column 3. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:234) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 32 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: iso19115.iso-19115.2.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: Server returned HTTP response code: 502 for URL: http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: Server returned HTTP response code: 502 for URL: http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 31 more Caused by: java.io.IOException: Server returned HTTP response code: 502 for URL: http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 36 more Caused by: java.io.IOException: Server returned HTTP response code: 502 for URL: http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1840) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 39 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: iceci.international-classification-of--external-causes-of-injuries.6.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: rao.rheumatoid-arthritis-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: cdao.comparative-data-analysis-ontology.7.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: dermlex.dermatology-lexicon.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: gpml.graphical-pathway-markup-language.317.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: fix.physico-chemical-methods-and-properties.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: onlira.ontology-of-liver-for-radiology.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: igto.scientific-evidence-based-genetic-testing-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: adalab-meta.adalab-meta-ontology.6.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: lipro.lipid-ontology.4.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://unbsj.biordf.net/lipids/lipid-maps-ontology.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://unbsj.biordf.net/lipids/lipid-maps-ontology.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 32 more Caused by: java.io.FileNotFoundException: http://unbsj.biordf.net/lipids/lipid-maps-ontology.owl at sun.reflect.GeneratedConstructorAccessor96.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 37 more Caused by: java.io.FileNotFoundException: http://unbsj.biordf.net/lipids/lipid-maps-ontology.owl at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 40 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bao.bioassay-ontology.29.orig PROCESSING: rdl.rdl.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: Server returned HTTP response code: 403 for URL: http://rds.posccaesar.org/2008/02/OWL/ISO-15926-2_2003 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: Server returned HTTP response code: 403 for URL: http://rds.posccaesar.org/2008/02/OWL/ISO-15926-2_2003 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 31 more Caused by: java.io.IOException: Server returned HTTP response code: 403 for URL: http://rds.posccaesar.org/2008/02/OWL/ISO-15926-2_2003 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 36 more Caused by: java.io.IOException: Server returned HTTP response code: 403 for URL: http://rds.posccaesar.org/2008/02/OWL/ISO-15926-2_2003 at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1840) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 39 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: aero.adverse-event-reporting-ontology.45.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://ogms.googlecode.com/svn/trunk/src/ontology/omre/OMRE_AEROImport.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://ogms.googlecode.com/svn/trunk/src/ontology/omre/OMRE_AEROImport.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 31 more Caused by: java.io.FileNotFoundException: http://ogms.googlecode.com/svn/trunk/src/ontology/omre/OMRE_AEROImport.owl at sun.reflect.GeneratedConstructorAccessor96.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 36 more Caused by: java.io.FileNotFoundException: http://ogms.googlecode.com/svn/trunk/src/ontology/omre/OMRE_AEROImport.owl at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 39 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: sitbac.situation-based-access-control-ontology.3.orig PROCESSING: edda.edda-study-designs-taxonomy.11.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: amino-acid.amino-acid-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: sse.surgical-secondary-events.2.orig ... merge successful. PROCESSING: pma.portfolio-management-application.4.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: ogmd.ontology-of-glucose-metabolism-disorder.31.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: cso.clinical-study-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ontodm-core.ontology-of-core-data-mining-entities.6.orig PROCESSING: genepio.genepio.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: norreg.norwegian-national-quality-registries--variabelbibliotek-for-medisinske-kvalitetsregistre.1.orig org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/home/zeus/experiments/bpdownload/repo/tmp/norreg.norwegian-national-quality-registries--variabelbibliotek-for-medisinske-kvalitetsregistre.1.orig 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@761eebe6 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@378bb786 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@36cb2b4a 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@3c064065 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@1c1f1894 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@3f0513a3 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@40176d04 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@761eebe6 Stack trace: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=2:column=17] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [line=2:column=17] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.verify(RDFParser.java:451) org.semanticweb.owlapi.rdf.rdfxml.parser.StartRDF.startElement(StartRDF.java:187) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@378bb786 Stack trace: org.xml.sax.SAXParseException; systemId: file:/home/zeus/experiments/bpdownload/repo/tmp/norreg.norwegian-national-quality-registries--variabelbibliotek-for-medisinske-kvalitetsregistre.1.orig; lineNumber: 419; columnNumber: 3; The element type "link" must be terminated by the matching end-tag "". org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) The element type "link" must be terminated by the matching end-tag "". 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.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@36cb2b4a Stack trace: Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@3c064065 Stack trace: Encountered '' 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: The element type "link" must be terminated by the matching end-tag "". [line 419, column 3] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) The element type "link" must be terminated by the matching end-tag "". [line 419, column 3] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:96) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:89) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) The element type "link" must be terminated by the matching end-tag "". org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@1c1f1894 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@3f0513a3 Stack trace: LINENO: 1 - Could not find tag separator ':' in line. LINE: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) LINENO: 1 - Could not find tag separator ':' in line. LINE: org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521) 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:197) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@40176d04 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Encountered " ">" " "" at line 1, column 1. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:234) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) PROCESSING: cyto.cytokine.27.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: vo.vaccine-ontology.246.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mfo.medaka-fish-anatomy-and-development-ontology.14.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: aura.kb_bio_101.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: fma.foundational-model-of-anatomy.20.orig PROCESSING: ocdm.ontology-of-craniofacial-development-and-malformation.2.orig /home/zeus/experiments/bpdownload/repo/tmp/ocdm.ontology-of-craniofacial-development-and-malformation.2.orig_unzipped/ocdm_v1.7.0/.DS_Store (Not a directory) Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. PROCESSING: tto.teleost-taxonomy-ontology.43.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: rpo.resource-of-asian-primary-immunodeficiency-diseases-rapid-phenotype-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: vt.vertebrate-trait-ontology.65.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: obcs.ontology-of-biological-and-clinical-statistics.13.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: lda.ontology-of-language-disorder-in-autism.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: uberon.uber-anatomy-ontology.251.orig PROCESSING: odnae.ontology-of-drug-neuropathy-adverse-events.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: dseo.data-science-education-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ros.radiation-oncology-structures-ontology.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: meo.metagenome-and-microbes-environmental-ontology.8.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: roo.radiation-oncology-ontology.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: internano.internano-nanomanufacturing-taxonomy.137.orig org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/home/zeus/experiments/bpdownload/repo/tmp/internano.internano-nanomanufacturing-taxonomy.137.orig 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@1efa1ac1 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@325b994f 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@7cb9b1d7 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@1a4ce845 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@4e2857b8 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@7596f19b 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@289c0e5b 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@1efa1ac1 Stack trace: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=65:column=5] Expecting an object element instead of character content. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [line=65:column=5] Expecting an object element instead of character content. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.verify(RDFParser.java:451) org.semanticweb.owlapi.rdf.rdfxml.parser.NodeElementList.characters(StartRDF.java:385) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.characters(RDFParser.java:213) org.apache.xerces.parsers.AbstractSAXParser.characters(Unknown Source) org.apache.xerces.impl.dtd.XMLDTDValidator.characters(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanContent(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.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@325b994f Stack trace: org.xml.sax.SAXParseException; systemId: file:/home/zeus/experiments/bpdownload/repo/tmp/internano.internano-nanomanufacturing-taxonomy.137.orig; lineNumber: 69; columnNumber: 11; The content of elements must consist of well-formed character data or markup. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) The content of elements must consist of well-formed character data or markup. 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.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.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@7cb9b1d7 Stack trace: Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@1a4ce845 Stack trace: Encountered '" " "" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) Encountered " ">" " "" at line 1, column 1. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:234) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) PROCESSING: uo.units-of-measurement-ontology.43.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ogms.ontology-for-general-medical-science.9.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: ocvdae.ontology-of-cardiovascular-drug-adverse-events.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bridg.biomedical-research-integrated-domain-group-model.1.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bcteo.bone-and-cartilage-tissue-engineering-ontology.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mineral.material-mineral.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: idoden.dengue-fever-ontology.6.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mods.mods-rdf-ontology.2.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: Server returned HTTP response code: 403 for URL: http://www.loc.gov/standards/mads/rdf/v1.rdf at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: Server returned HTTP response code: 403 for URL: http://www.loc.gov/standards/mads/rdf/v1.rdf at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 31 more Caused by: java.io.IOException: Server returned HTTP response code: 403 for URL: http://www.loc.gov/standards/mads/rdf/v1.rdf at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 36 more Caused by: java.io.IOException: Server returned HTTP response code: 403 for URL: http://www.loc.gov/standards/mads/rdf/v1.rdf at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1840) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 39 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: matrrock.material-rock.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: exact.an-ontology-for-experimental-actions.2.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://ontofox.hegroup.org/ztx3ioxo.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.owlxml.parser.OWLImportsHandler.endElement(PARSER_OWLXMLVocabulary.java:3004) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:422) 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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:60) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://ontofox.hegroup.org/ztx3ioxo.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 27 more Caused by: java.io.FileNotFoundException: http://ontofox.hegroup.org/ztx3ioxo.owl at sun.reflect.GeneratedConstructorAccessor96.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 32 more Caused by: java.io.FileNotFoundException: http://ontofox.hegroup.org/ztx3ioxo.owl at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 35 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bro_acronym.bro_name.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: canco.cancer-chemoprevention-ontology.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: spto.solanaceae-phenotype-ontology.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mixs.minimal-information-about-any-sequence-ontology.5.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: lbo.livestock-breed-ontology.8.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bof.biodiversity-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: spo.skin-physiology-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: snpo.single-nucleotide-polymorphism-snp-ontology.4.orig PROCESSING: nemo.neural-electromagnetic-ontology.24.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: Problem parsing http://www.co-ode.org/ontologies/amino-acid/2005/10/11/amino-acid.owl 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@a0e9f2e 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@5c007ab8 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@228969f9 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@19208176 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@7a660e4a 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@523a0b68 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@361781e7 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@a0e9f2e Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/amino-acid/2005/10/11/amino-acid.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:78) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. 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.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@5c007ab8 Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/amino-acid/2005/10/11/amino-acid.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@228969f9 Stack trace: Encountered " " "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " " "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@19208176 Stack trace: Encountered ' ' at line 1 column 3. Expected either 'Ontology:' or 'Prefix:' (Line 1) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:102) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) White spaces are required after keyword PUBLIC in DOCTYPE decl. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@7a660e4a Stack trace: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@523a0b68 Stack trace: LINENO: 1 - Could not find tag separator ':' in line. LINE: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) LINENO: 1 - Could not find tag separator ':' in line. LINE: org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521) 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.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@361781e7 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 3. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " ">" " "" at line 1, column 3. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://www.co-ode.org/ontologies/amino-acid/2005/10/11/amino-acid.owl 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@a0e9f2e 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@5c007ab8 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@228969f9 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@19208176 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@7a660e4a 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@523a0b68 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@361781e7 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@a0e9f2e Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/amino-acid/2005/10/11/amino-acid.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:78) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) org.apache.xerces.impl.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@5c007ab8 Stack trace: org.xml.sax.SAXParseException; systemId: http://www.co-ode.org/ontologies/amino-acid/2005/10/11/amino-acid.owl; lineNumber: 1; columnNumber: 24; White spaces are required after keyword PUBLIC in DOCTYPE decl. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. 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.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@228969f9 Stack trace: Encountered " " "" at line 1, column 3. Was expecting one of: "Ontology" ... "Prefix" ... (Line 0) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:79) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " " "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@19208176 Stack trace: Encountered ' ' at line 1 column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) White spaces are required after keyword PUBLIC in DOCTYPE decl. [line 1, column 24] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) White spaces are required after keyword PUBLIC in DOCTYPE decl. 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.XMLScanner.scanExternalID(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl.scanDoctypeDecl(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@7a660e4a Stack trace: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 3. Was expecting one of: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:90) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered "" at line 1, column 3. 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@523a0b68 Stack trace: LINENO: 1 - Could not find tag separator ':' in line. LINE: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) LINENO: 1 - Could not find tag separator ':' in line. LINE: org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1501) org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:897) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:528) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:521) 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.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@361781e7 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 3. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " ">" " "" at line 1, column 3. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:234) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 31 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: galen.galen-ontology.1.orig PROCESSING: ordo.orphanet-rare-disease-ontology.10.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: cogat.cognitive-atlas-ontology.7.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: nifstd.neuroscience-information-framework-nif-standard-ontology.21.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: spd.spider-ontology.23.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mera.medical-educational-resource-aggregator.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: obi_bcgo.beta-cell-genomics-ontology.14.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ptrans.pathogen-transmission-ontology.14.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bno.bionutrition-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: cco.cell-cycle-ontology.9.orig PROCESSING: ontoad.bilingual-ontology-of-alzheimers-disease-and-related-diseases.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: legalapa.legalapa.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: /Users/olgagiraldo/Desktop/apaMasiveOUT/Adjudication_cluster.owl (No such file or directory) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.owlxml.parser.OWLImportsHandler.endElement(PARSER_OWLXMLVocabulary.java:3004) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:422) 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 org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:60) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: /Users/olgagiraldo/Desktop/apaMasiveOUT/Adjudication_cluster.owl (No such file or directory) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 27 more Caused by: java.io.FileNotFoundException: /Users/olgagiraldo/Desktop/apaMasiveOUT/Adjudication_cluster.owl (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.(FileInputStream.java:138) at java.io.FileInputStream.(FileInputStream.java:93) at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90) at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:188) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 32 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: qudt.quantities-units-dimensions-and-types-ontology.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ogr.ontology-of-geographical-region.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: soy.soy-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: sp.smart-protocols.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: so.sequence-types-and-features-ontology.220.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: ogg.ontology-of-genes-and-genomes.3.orig PROCESSING: radlex.radiology-lexicon.37.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: ncit.national-cancer-institute-thesaurus.47.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ogi.ontology-for-genetic-interval.18.orig ... merge successful. ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: acgt-mo.cancer-research-and-management-acgt-master-ontology.2.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: peao.plant-experimental-assay-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: bmt.biomedical-topics.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: sweet.semantic-web-for-earth-and-environment-technology-ontology.1.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: fb-cv.flybase-controlled-vocabulary.20.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: go-ext.gene-ontology-extension.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: apaonto.psychology-ontology.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv java.io.FileNotFoundException: http://data.bioontology.org/ontologies/MIRO/submissions/1160/download at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at owl.cs.bioportal.download.BioPortalDownloadOntology.download(BioPortalDownloadOntology.java:148) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:81) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) java.lang.NullPointerException at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:2146) at org.apache.commons.io.IOUtils.copy(IOUtils.java:2102) at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:2123) at org.apache.commons.io.IOUtils.copy(IOUtils.java:2078) at org.apache.commons.io.FileUtils.copyToFile(FileUtils.java:1554) at org.apache.commons.io.FileUtils.copyInputStreamToFile(FileUtils.java:1528) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:82) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) PROCESSING: bcgo.breast-cancer-grading-ontology.2.orig Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: ncco.nursing-care-coordination-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: cisaviado.ciona-savignyi-anatomy-and-development-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: tron.tribolium-ontology.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: Problem parsing http://www.owl-ontologies.com/2005/08/07/xsp.owl 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@2b6b6efa 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@6867e410 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@180b4b58 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@49bcfe32 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@71e3deae 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@751dfa8 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@1558bd8 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@2b6b6efa Stack trace: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=2:column=280] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) [line=2:column=280] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.verify(RDFParser.java:451) org.semanticweb.owlapi.rdf.rdfxml.parser.StartRDF.startElement(StartRDF.java:187) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@6867e410 Stack trace: org.xml.sax.SAXParseException; systemId: http://www.owl-ontologies.com/2005/08/07/xsp.owl; lineNumber: 3; columnNumber: 544; The reference to entity "b" must end with the ';' delimiter. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) The reference to entity "b" must end with the ';' delimiter. 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.XMLDocumentFragmentScannerImpl.scanEntityReference(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@180b4b58 Stack trace: Encountered " " "" at line 1, column 1. Was expecting one of: "Ontology" ... "Prefix" ... (Line 0) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:79) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@49bcfe32 Stack trace: Encountered '' 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: The declaration for the entity "ContentType" must end with '>'. [line 81, column 5] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) The declaration for the entity "ContentType" must end with '>'. [line 81, column 5] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) The declaration for the entity "ContentType" must end with '>'. 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.XMLDTDScannerImpl.scanEntityDecl(Unknown Source) org.apache.xerces.impl.XMLDTDScannerImpl.scanDecls(Unknown Source) org.apache.xerces.impl.XMLDTDScannerImpl.scanDTDExternalSubset(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@71e3deae Stack trace: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 1. Was expecting one of: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:90) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@751dfa8 Stack trace: LINENO: 3 - expected newline or end of line but found: catch(err){}}try{window.onload=handleABPDetect();}catch(err){}owl-ontologies.com LINE: owl-ontologies.com org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) LINENO: 3 - expected newline or end of line but found: catch(err){}}try{window.onload=handleABPDetect();}catch(err){}owl-ontologies.com LINE: owl-ontologies.com 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.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:58) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@1558bd8 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " ">" " "" at line 1, column 1. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://www.owl-ontologies.com/2005/08/07/xsp.owl Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation. The following parsers were tried: 1) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@2b6b6efa 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@6867e410 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@180b4b58 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@49bcfe32 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d 12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@71e3deae 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@751dfa8 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@1558bd8 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@2b6b6efa Stack trace: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=2:column=280] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) [line=2:column=280] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.verify(RDFParser.java:451) org.semanticweb.owlapi.rdf.rdfxml.parser.StartRDF.startElement(StartRDF.java:187) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@6867e410 Stack trace: org.xml.sax.SAXParseException; systemId: http://www.owl-ontologies.com/2005/08/07/xsp.owl; lineNumber: 3; columnNumber: 544; The reference to entity "b" must end with the ';' delimiter. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) The reference to entity "b" must end with the ';' delimiter. 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.XMLDocumentFragmentScannerImpl.scanEntityReference(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@180b4b58 Stack trace: Encountered " " "" at line 1, column 1. Was expecting one of: "Ontology" ... "Prefix" ... (Line 0) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:79) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " " "" 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@49bcfe32 Stack trace: Encountered '' 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Quads (mimeTypes=text/x-nquads; ext=nq) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/JSON (mimeTypes=application/rdf+json; ext=rj) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N-Triples (mimeTypes=text/plain; ext=nt) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format TriG (mimeTypes=application/x-trig; ext=trig) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format BinaryRDF (mimeTypes=application/x-binary-rdf; ext=brf) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format JSON-LD (mimeTypes=application/ld+json; ext=jsonld) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format N3 (mimeTypes=text/n3, text/rdf+n3; ext=n3) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDF/XML (mimeTypes=application/rdf+xml, application/xml; ext=rdf, rdfs, owl, xml) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.openrdf.rio.RDFParseException: The declaration for the entity "ContentType" must end with '>'. [line 81, column 5] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) The declaration for the entity "ContentType" must end with '>'. [line 81, column 5] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487) org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123) org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) The declaration for the entity "ContentType" must end with '>'. 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.XMLDTDScannerImpl.scanEntityDecl(Unknown Source) org.apache.xerces.impl.XMLDTDScannerImpl.scanDecls(Unknown Source) org.apache.xerces.impl.XMLDTDScannerImpl.scanDTDExternalSubset(Unknown Source) org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@71e3deae Stack trace: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 1. Was expecting one of: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:90) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@751dfa8 Stack trace: LINENO: 3 - expected newline or end of line but found: catch(err){}}try{window.onload=handleABPDetect();}catch(err){}owl-ontologies.com LINE: owl-ontologies.com org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) LINENO: 3 - expected newline or end of line but found: catch(err){}}try{window.onload=handleABPDetect();}catch(err){}owl-ontologies.com LINE: owl-ontologies.com 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.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:281) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:58) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@1558bd8 Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" " "" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:273) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) Encountered " ">" " "" at line 1, column 1. Was expecting: 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:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:207) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) No parser factory available for RDF format RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.openrdf.rio.Rio.createParser(Rio.java:198) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:241) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:234) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 31 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: surgical.nurse-surgical.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: wsio.web-service-interaction-ontology.4.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: hupson.human-physiology-simulation-ontology.1.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: cno.computational-neuroscience-ontology.8.orig PROCESSING: ero.eagle-i-research-resource-ontology.14.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: http://www.obofoundry.org/ro/ro.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1537) at org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:194) at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1545) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:370) at org.semanticweb.owlapi.rdf.rdfxml.parser.EmptyPropertyElement.startElement(StartRDF.java:236) at org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:658) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.emptyElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(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 org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://www.obofoundry.org/ro/ro.owl at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 32 more Caused by: java.io.FileNotFoundException: http://www.obofoundry.org/ro/ro.owl at sun.reflect.GeneratedConstructorAccessor96.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1885) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1884) at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1457) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 37 more Caused by: java.io.FileNotFoundException: http://www.obofoundry.org/ro/ro.owl at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ... 40 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: legalapatest2.apalegal.1.orig org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: alexandergarcia.name at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) at org.semanticweb.owlapi.owlxml.parser.OWLImportsHandler.endElement(PARSER_OWLXMLVocabulary.java:3004) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:422) 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$JAXPSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) at org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:60) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) at owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: alexandergarcia.name at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ... 27 more Caused by: java.net.UnknownHostException: alexandergarcia.name at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:175) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1169) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1105) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:999) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:933) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:102) at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ... 32 more Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: nidm-results.nidm-results.2.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_orig_metadata.csv PROCESSING: mat.minimal-anatomical-terminology.3.orig ... merge successful. Saved CSV to /home/zeus/experiments/bpdownload/repo/metadata/bp_owlxml_metadata.csv PROCESSING: gvp.getty-vocabulary-program-ontology.1.orig org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/home/zeus/experiments/bpdownload/repo/tmp/gvp.getty-vocabulary-program-ontology.1.orig 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@607a74f0 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@2f2986bf 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@1cc7aa5e 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@4ed64803 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 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.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@717cbb54 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@48eff830 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@7691961f 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@607a74f0 Stack trace: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=2:column=7] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(FutureTask.java:266) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [line=2:column=7] Expecting rdf:RDF element. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.verify(RDFParser.java:451) org.semanticweb.owlapi.rdf.rdfxml.parser.StartRDF.startElement(StartRDF.java:187) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201) org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@2f2986bf Stack trace: org.xml.sax.SAXParseException; systemId: file:/home/zeus/experiments/bpdownload/repo/tmp/gvp.getty-vocabulary-program-ontology.1.orig; lineNumber: 46; columnNumber: 7; The element type "link" must be terminated by the matching end-tag "". org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1016) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:98) owl.cs.bioportal.download.BioPortalDownloadOntology.call(BioPortalDownloadOntology.java:23) java.util.concurrent.FutureTask.run(Fut