Comments (2)
Loading GEO failed.
The error messages:
Loading RDF store:
geo: loading data from http://purl.obolibrary.org/obo/geo.owl
geo: getting final url http://purl.obolibrary.org/obo/geo.owl
Coult not load ontology:
org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: http://www.ifomis.org/bfo/1.1 Cause: Problem parsing http://www.ifomis.org/bfo/1.1
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:
- RDFXMLParser
- OWLXMLParser
- OWLFunctionalSyntaxOWLParser
- TurtleOntologyParser
- OWLOBOParser
- KRSS2OWLParser
- ManchesterOWLSyntaxOntologyParser
Detailed logs:
Parser: RDFXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
Parser: OWLXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
Parser: OWLFunctionalSyntaxOWLParser
Encountered " "< "" at line 1, column 1.
Was expecting:
"Ontology" ...
(Line 0)
Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:
Parser: OWLOBOParser
org.coode.owlapi.obo.parser.TokenMgrError: Lexical error at line 1, column 51. Encountered: "\n" (10), after : ""
Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" " "" at line 1, column 1.
Was expecting:
Parser: ManchesterOWLSyntaxOntologyParser
Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1077)
at org.coode.owlapi.owlxmlparser.OWLImportsHandler.endElement(OWLImportsHandler.java:28)
at org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:895)
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 javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
at org.coode.owlapi.owlxmlparser.OWLXMLParser.parse(OWLXMLParser.java:47)
at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:687)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:628)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:602)
at org.hegroup.rdfstore.OWLMerge.main(OWLMerge.java:65)
Caused by: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://www.ifomis.org/bfo/1.1
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:
- RDFXMLParser
- OWLXMLParser
- OWLFunctionalSyntaxOWLParser
- TurtleOntologyParser
- OWLOBOParser
- KRSS2OWLParser
- ManchesterOWLSyntaxOntologyParser
Detailed logs:
Parser: RDFXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
Parser: OWLXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
Parser: OWLFunctionalSyntaxOWLParser
Encountered " "< "" at line 1, column 1.
Was expecting:
"Ontology" ...
(Line 0)
Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:
Parser: OWLOBOParser
org.coode.owlapi.obo.parser.TokenMgrError: Lexical error at line 1, column 51. Encountered: "\n" (10), after : ""
Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" " "" at line 1, column 1.
Was expecting:
Parser: ManchesterOWLSyntaxOntologyParser
Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1)
at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:197)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:687)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:628)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1045)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1070)
... 21 more
geo: loading data from http://purl.obolibrary.org/obo/geo.owl
geo: getting final url http://purl.obolibrary.org/obo/geo.owl
Coult not load ontology:
org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: http://www.ifomis.org/bfo/1.1 Cause: Problem parsing http://www.ifomis.org/bfo/1.1
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:
- RDFXMLParser
- OWLXMLParser
- OWLFunctionalSyntaxOWLParser
- TurtleOntologyParser
- OWLOBOParser
- KRSS2OWLParser
- ManchesterOWLSyntaxOntologyParser
Detailed logs:
Parser: RDFXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
Parser: OWLXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
Parser: OWLFunctionalSyntaxOWLParser
Encountered " "< "" at line 1, column 1.
Was expecting:
"Ontology" ...
(Line 0)
Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:
Parser: OWLOBOParser
org.coode.owlapi.obo.parser.TokenMgrError: Lexical error at line 1, column 51. Encountered: "\n" (10), after : ""
Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" " "" at line 1, column 1.
Was expecting:
Parser: ManchesterOWLSyntaxOntologyParser
Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1077)
at org.coode.owlapi.owlxmlparser.OWLImportsHandler.endElement(OWLImportsHandler.java:28)
at org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:895)
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 javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
at org.coode.owlapi.owlxmlparser.OWLXMLParser.parse(OWLXMLParser.java:47)
at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:687)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:628)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:602)
at org.hegroup.rdfstore.OWLMerge.main(OWLMerge.java:65)
Caused by: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://www.ifomis.org/bfo/1.1
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:
- RDFXMLParser
- OWLXMLParser
- OWLFunctionalSyntaxOWLParser
- TurtleOntologyParser
- OWLOBOParser
- KRSS2OWLParser
- ManchesterOWLSyntaxOntologyParser
Detailed logs:
Parser: RDFXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
Parser: OWLXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
Parser: OWLFunctionalSyntaxOWLParser
Encountered " "< "" at line 1, column 1.
Was expecting:
"Ontology" ...
(Line 0)
Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:
Parser: OWLOBOParser
org.coode.owlapi.obo.parser.TokenMgrError: Lexical error at line 1, column 51. Encountered: "\n" (10), after : ""
Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" " "" at line 1, column 1.
Was expecting:
Parser: ManchesterOWLSyntaxOntologyParser
Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1)
at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:197)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:687)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:628)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1045)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1070)
... 21 more
Failed to download owl file!
Done!
Oliver
From: Melanie Courtot [mailto:[email protected]]
Sent: Wednesday, May 13, 2015 6:32 PM
To: ontoden/ontobee
Subject: [ontobee] Loading GEO on Ontobee (#41)
From http://purl.obolibrary.org/obo/geo.owl
Thanks,
Melanie
—
Reply to this email directly or view it on GitHubhttps://github.com//issues/41.
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
from ontobee.
GEO is already loaded into Ontobee.
I am closing this issue. Thanks.
from ontobee.
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