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[protege-owl] Error while parsing ontology created in Protege4 with OWLAPI

Timothy Redmond tredmond at stanford.edu
Thu Aug 27 14:36:10 PDT 2009


Thank you for such a clear report of the problem.  I was able to
replicate it based on your information.

When I built and ran the program with an owlapi jar file freshly built
(using ant) the program ran fine.  But when I used the the jar file [1]
I got the errors below.

So it is not clear to me what it is about the jar file [1] that would
give rise to these errors.  Strange.  But hopefully if you build the owl
api jar file yourself it will run fine.

-Timothy


[1]
http://maven.topazproject.org/maven2/owlapi/owlapi/2.2.0/owlapi-2.2.0.jar




Problem parsing http://student.agh.edu.pl/~jwa/owl/Shapes.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.coode.owl.rdfxml.parser.RDFXMLParser
2) org.coode.owl.owlxmlparser.OWLXMLParser
3) org.coode.owl.functionalparser.OWLFunctionalSyntaxOWLParser
4) uk.ac.manchester.cs.owl.turtle.parser.TurtleOntologyParser
5) org.coode.manchesterowlsyntax.ManchesterOWLSyntaxOntologyParser
6) org.coode.obo.parser.OWLOBOParser
7) de.uulm.ecs.ai.owl.krssparser.KRSS2OWLParser


Detailed logs:
--------------------------------------------------------------------------------
Parser class: org.coode.owl.rdfxml.parser.RDFXMLParser
edu.unika.aifb.rdf.api.syntax.RDFParserException: [line=22:column=68]
Expecting rdf:RDF element.

--------------------------------------------------------------------------------
Parser class: org.coode.owl.owlxmlparser.OWLXMLParser
(Current element Class

--------------------------------------------------------------------------------
Parser class:
org.coode.owl.functionalparser.OWLFunctionalSyntaxOWLParser
org.coode.owl.functionalparser.ParseException: Encountered "<" at line
1, column 1.
Was expecting one of:
    "Ontology" ...
    "Namespace" ...
     (Line 0)

--------------------------------------------------------------------------------
Parser class: uk.ac.manchester.cs.owl.turtle.parser.TurtleOntologyParser
java.net.URISyntaxException: Illegal character in query at index 4: ?xml
version="1.0"?

--------------------------------------------------------------------------------
Parser class:
org.coode.manchesterowlsyntax.ManchesterOWLSyntaxOntologyParser
org.semanticweb.owl.expression.ParserException: Encountered <?xml at
line 0 column 0. Expected one of:
	ValuePartition:
	Individual:
	DataProperty:
	Imports:
	ObjectProperty:
	Class:


--------------------------------------------------------------------------------
Parser class: org.coode.obo.parser.OWLOBOParser
org.coode.obo.parser.ParseException: Encountered "<!DOCTYPE Ontology "
at line 4, column 1.
Was expecting:
    "\n" ...
    

--------------------------------------------------------------------------------
Parser class: de.uulm.ecs.ai.owl.krssparser.KRSS2OWLParser
de.uulm.ecs.ai.owl.krssparser.ParseException: Encountered "<?xml
version=\"1.0\"?>" at line 1, column 1.
Was expecting one of:
    <EOF> 
    "(" ...
    "end-tbox" ...
    "end-abox" ...
    


On Thu, 2009-08-27 at 19:20 +0200, jwa at student.agh.edu.pl wrote:
> One more,
> 
> I have created sample ontology in Protege 4, and sample code of loading
> that ontology in my program. I generates error.
> 
> String strPhysicalURIofOntology =
> "http://student.agh.edu.pl/~jwa/owl/Shapes.owl";
> 
> OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
> URI uriOntology = URI.create(strPhysicalURIofOntology);
> 
> try {
> 	manager.setSilentMissingImportsHandling(true);
> 	manager.loadOntology(uriOntology);  //error
> } catch (OWLOntologyCreationException ex) {
> 	System.out.print(ex.getMessage());
> }
> 
> Thaks in advance
> 
> > Hello
> >
> > Thank You very much for checking that.
> >
> > I have also no problem with the ontology when I'm using Protege 4 (113).
> > The OWLAPI is causing problems in my simple program.
> >
> > I' using owlapi-2.2.0.jar from http://maven.topazproject.org/maven2, I'm
> > using maven and I've choosen the 2.2.0 version to be automatically
> > downloaded. In attachement is screen from dependencies names and versions
> > which I've used.
> >
> > Take care.
> >
> >> Hi jwa,
> >>
> >> ok, so your points 1 and 2 show that I was wrong with my advise to add
> >> one more slash behind "file:/" on Windows, sorry.
> >>
> >> I've tried to open your ontology, whose link you sent me privately, in
> >> Protégé 4 build 113 and didn't get any errors. Since your problems
> >> occur with the OWL API, I suspect you're using a different, probably
> >> older, version of the OWL API than the one bundled with the Protégé
> >> version you used to create the ontology.
> >>
> >> Can you please post the build number for Protégé and the OWL API
> >> version number?
> >>
> >> Cheers
> >>
> >> Thomas
> >>
> >> On 25 Aug 2009, at 23:13, jwa at student.agh.edu.pl wrote:
> >>
> >>> 1. first execution:
> >>>
> >>> OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
> >>> URI physicalURI = URI.create("file://C:/Users/jwa/Desktop/myont.owl");
> >>> OWLOntology ontology =
> >>> manager.loadOntologyFromPhysicalURI(physicalURI);
> >>>
> >>> result:
> >>>
> >>> The ontology could not be created: C
> >>>
> >>> 2. second execution
> >>>
> >>> OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
> >>> URI physicalURI = URI.create("file:/C:/Users/jwa/Desktop/myont.owl");
> >>> OWLOntology ontology =
> >>> manager.loadOntologyFromPhysicalURI(physicalURI);
> >>>
> >>> result:
> >>>
> >>> The ontology could not be created: Problem parsing
> >>> file:/C:/Users/jwa/Desktop/myont.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.coode.owl.rdfxml.parser.RDFXMLParser
> >>> 2) org.coode.owl.owlxmlparser.OWLXMLParser
> >>> 3) org.coode.owl.functionalparser.OWLFunctionalSyntaxOWLParser
> >>> 4) uk.ac.manchester.cs.owl.turtle.parser.TurtleOntologyParser
> >>> 5) org.coode.manchesterowlsyntax.ManchesterOWLSyntaxOntologyParser
> >>> 6) org.coode.obo.parser.OWLOBOParser
> >>> 7) de.uulm.ecs.ai.owl.krssparser.KRSS2OWLParser
> >>>
> >>>
> >>> Detailed logs:
> >>> --------------------------------------------------------------------------------
> >>> Parser class: org.coode.owl.rdfxml.parser.RDFXMLParser
> >>> org.coode.owl.rdfxml.parser.OWLRDFParserException: Unable to
> >>> determine the
> >>> type of restriction!
> >>>
> >>> --------------------------------------------------------------------------------
> >>> Parser class: org.coode.owl.owlxmlparser.OWLXMLParser
> >>> (Current element RDF
> >>>
> >>> --------------------------------------------------------------------------------
> >>> Parser class:
> >>> org.coode.owl.functionalparser.OWLFunctionalSyntaxOWLParser
> >>> org.coode.owl.functionalparser.ParseException: Encountered "<" at
> >>> line 1,
> >>> column 1.
> >>> Was expecting one of:
> >>>    "Ontology" ...
> >>>    "Namespace" ...
> >>>     (Line 0)
> >>>
> >>> --------------------------------------------------------------------------------
> >>> Parser class:
> >>> uk.ac.manchester.cs.owl.turtle.parser.TurtleOntologyParser
> >>> java.net.URISyntaxException: Illegal character in query at index 4: ?
> >>> xml
> >>> version="1.0"?
> >>>
> >>> --------------------------------------------------------------------------------
> >>> Parser class:
> >>> org.coode.manchesterowlsyntax.ManchesterOWLSyntaxOntologyParser
> >>> org.semanticweb.owl.expression.ParserException: Encountered <?xml at
> >>> line
> >>> 0 column 0. Expected one of:
> >>> 	Individual:
> >>> 	Class:
> >>> 	ObjectProperty:
> >>> 	Imports:
> >>> 	DataProperty:
> >>> 	ValuePartition:
> >>>
> >>>
> >>> --------------------------------------------------------------------------------
> >>> Parser class: org.coode.obo.parser.OWLOBOParser
> >>> org.coode.obo.parser.ParseException: Encountered "<!DOCTYPE rdf" at
> >>> line
> >>> 4, column 1.
> >>> Was expecting:
> >>>    "\n" ...
> >>>
> >>>
> >>> --------------------------------------------------------------------------------
> >>> Parser class: de.uulm.ecs.ai.owl.krssparser.KRSS2OWLParser
> >>> de.uulm.ecs.ai.owl.krssparser.ParseException: Encountered "<?xml
> >>> version=\"1.0\"?>" at line 1, column 1.
> >>> Was expecting one of:
> >>>    <EOF>
> >>>    "(" ...
> >>>    "end-tbox" ...
> >>>    "end-abox" ...
> >>>
> >>>> This seems to be a problem with the file name:
> >>>>
> >>>>      file:/C:/Users/jwa/myont.owl
> >>>>
> >>>> I think under Windows it must be file:// plus the path and file name.
> >>>> So if you try to change the parameter for
> >>>> loadOntologyFromPhysicalURI(..), you might be able to solve the
> >>>> problem.
> >>>>
> >>>> Otherwise, please post the complete line that contains the call to
> >>>> loadOntologyFromPhysicalURI.
> >>>>
> >>>> Cheers
> >>>>
> >>>> Thomas
> >>>>
> >>>> On 25 Aug 2009, at 20:24, jwa at student.agh.edu.pl wrote:
> >>>>
> >>>>> Hello
> >>>>>
> >>>>> For example: I saved my ontology in Manchester OWL syntax format,
> >>>>> and
> >>>>> while invoking loadOntologyFromPhysicalURI(..), the following error
> >>>>> occures:
> >>>>>
> >>>>> ##############
> >>>>> The ontology could not be created: Problem parsing
> >>>>> file:/C:/Users/jwa/myont.owl
> >>>>> Could not parse ontology.  Either a suitable parser could not be
> >>>>> found, or
> >>>>> parsing failed.
> >>>>> ...
> >>>>> --------------------------------------------------------------------------
> >>>>> Parser class:
> >>>>> org.coode.manchesterowlsyntax.ManchesterOWLSyntaxOntologyParser
> >>>>> org.semanticweb.owl.expression.ParserException: Encountered
> >>>>> <http://www.w3.org/2006/12/owl2-xml#> at line 0 column 19. Expected
> >>>>> one
> >>>>> of:
> >>>>> 	=
> >>>>>
> >>>>> --------------------------------------------------------------------------
> >>>>> ...
> >>>>> ##############
> >>>>>
> >>>>> Thanks in advice
> >>>>>
> >>>>>>
> >>>>>> First, Protege 4 loads and saves ontologies using the owlapi.  So
> >>>>>> ontologies that you can load in Protege 4 certainly will load in
> >>>>>> the
> >>>>>> owl api.
> >>>>>>
> >>>>>> You need to provide some information about the error that you are
> >>>>>> seeing.  My first guess - based only on information that you have
> >>>>>> provided - is that you are having trouble with imports resolution.
> >>>>>> Protege 4 handles problems with an import gracefully but if you
> >>>>>> simply
> >>>>>> load an ontology with loadOntologyFromPhysicalURI an import that
> >>>>>> can't
> >>>>>> be found it will fail:
> >>>>>>
> >>>>>>   Parser: RDFXMLParser
> >>>>>>   org.semanticweb.owl.io.OWLOntologyCreationIOException:
> >>>>>> protege.stanford.edu
> >>>>>>
> >>>>>> If this is your problem then it can be easily fixed.
> >>>>>>
> >>>>>> -Timothy
> >>>>>>
> >>>>>>
> >>>>>> On Aug 24, 2009, at 5:37 PM, jwa at student.agh.edu.pl wrote:
> >>>>>>
> >>>>>>> Hello
> >>>>>>>
> >>>>>>> Is there any way to load an ontology, created in Protege 4, with
> >>>>>>> OWLAPI
> >>>>>>> (http://owlapi.sourceforge.net/) ?
> >>>>>>> The standard ontology from example
> >>>>>>> ("http://www.co-ode.org/ontologies/pizza/2007/02/12/pizza.owl") of
> >>>>>>> course
> >>>>>>> loads perfectly, but if I try to create another, simple ontology,
> >>>>>>> loading
> >>>>>>> fails on function loadOntologyFromPhysicalURI(..). I have tried to
> >>>>>>> load ontology in all output formats, which Protege provides, and
> >>>>>>> all
> >>>>>>> have
> >>>>>>> failed. (Protege didn't show any errors in his ontology, and read
> >>>>>>> and
> >>>>>>> write the ontology correttly).
> >>>>>>>
> >>>>>>> Thanks in advance.
> >>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> protege-owl mailing list
> >>>>>>> protege-owl at lists.stanford.edu
> >>>>>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >>>>>>>
> >>>>>>> Instructions for unsubscribing:
> >>>>>>> http://protege.stanford.edu/doc/faq.html#01a.03
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> protege-owl mailing list
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> >>>>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >>>>>>
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> >>>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
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> >>>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >>>>>
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> >>>>> http://protege.stanford.edu/doc/faq.html#01a.03
> >>>>
> >>>> +
> >>>> ----------------------------------------------------------------------+
> >>>> |  Dr Thomas Schneider                    schneider (at)
> >>>> cs.man.ac.uk  |
> >>>> |  School of Computer Science       http://www.cs.man.ac.uk/
> >>>> ~schneidt  |
> >>>> |  Kilburn Building, Room 2.114                 phone +44 161
> >>>> 2756136  |
> >>>> |  University of
> >>>> Manchester                                            |
> >>>> |  Oxford Road                                             _///
> >>>> _       |
> >>>> |  Manchester M13 9PL
> >>>> (o~o)       |
> >>>> +-----------------------------------------------------oOOO--(_)--
> >>>> OOOo--+
> >>>>
> >>>> Golant (adj.)
> >>>>   Blank, sly and faintly embarrassed. Pertaining to the expression
> >>>> seen
> >>>>   on the face of someone who has clearly forgotten your name.
> >>>>
> >>>>                   Douglas Adams, John Lloyd: The Deeper Meaning of
> >>>> Liff
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> protege-owl mailing list
> >>>> protege-owl at lists.stanford.edu
> >>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >>>>
> >>>> Instructions for unsubscribing:
> >>>> http://protege.stanford.edu/doc/faq.html#01a.03
> >>>>
> >>>
> >>>
> >>> _______________________________________________
> >>> protege-owl mailing list
> >>> protege-owl at lists.stanford.edu
> >>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >>>
> >>> Instructions for unsubscribing:
> >>> http://protege.stanford.edu/doc/faq.html#01a.03
> >>
> >> +----------------------------------------------------------------------+
> >> |  Dr Thomas Schneider                    schneider (at) cs.man.ac.uk  |
> >> |  School of Computer Science       http://www.cs.man.ac.uk/~schneidt  |
> >> |  Kilburn Building, Room 2.114                 phone +44 161 2756136  |
> >> |  University of Manchester                                            |
> >> |  Oxford Road                                             _///_       |
> >> |  Manchester M13 9PL                                      (o~o)       |
> >> +-----------------------------------------------------oOOO--(_)--OOOo--+
> >>
> >> Golant (adj.)
> >>    Blank, sly and faintly embarrassed. Pertaining to the expression seen
> >>    on the face of someone who has clearly forgotten your name.
> >>
> >>                    Douglas Adams, John Lloyd: The Deeper Meaning of Liff
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> protege-owl mailing list
> >> protege-owl at lists.stanford.edu
> >> https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >>
> >> Instructions for unsubscribing:
> >> http://protege.stanford.edu/doc/faq.html#01a.03
> >>
> > _______________________________________________
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> > https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
> > Instructions for unsubscribing:
> > http://protege.stanford.edu/doc/faq.html#01a.03
> >
> 
> 
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