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

jwa at student.agh.edu.pl jwa at student.agh.edu.pl
Sat Aug 29 08:31:28 PDT 2009


Thanks for that clue. It's working now :)

Have a nice day.

>
> 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
>> >> ProtĂŠgĂŠ 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 ProtĂŠgĂŠ
>> >> version you used to create the ontology.
>> >>
>> >> Can you please post the build number for ProtĂŠgĂŠ 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
>> >>>>>>
>> >>>>>> _______________________________________________
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>> >>>>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>> >>>>>>
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>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>> _______________________________________________
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>> >>>>>
>> >>>>> Instructions for unsubscribing:
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>> >>>>
>> >>>> +
>> >>>> ----------------------------------------------------------------------+
>> >>>> |  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
>> >>
>> > _______________________________________________
>> > 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:
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>
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