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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
Tue Aug 25 14:13:41 PDT 2009


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.
>>>>
>>>>
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>>
>>
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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                                            |
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