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[protege-discussion] a simple questions about owl programming

Timothy Redmond tredmond at stanford.edu
Tue Nov 23 09:16:11 PST 2010


I see you have some questions spanning a few days - I will go through 
them in reverse order.

>  but it can't be processed by the codes PropertyValuee.java, as the 
> same time family.owl can be. I'm so confused by this.  does anybody 
> give me a hint? And the error code is :

The errors that you are reporting are syntax errors coming from the 
Manchester OWL api. Your first snippet of code is based on the Protege 3 
OWL api.  It is a bit surprising but not amazing that Protege 3 can work 
with the ontology but the Manchester OWL finds a syntax error.  I 
believe that the Manchester OWL api is probably right - there is a 
problem with the ontology that it is trying to parse.  In particular the 
rdf error is probably the right one:

> Parser: RDFXMLParser
> org.xml.sax.SAXParseException: The value of attribute "rdf:resource" 
> associated with an element type "rdfs:subClassOf" must not contain the 
> '<' character.

If you send the ontology that the Manchester OWL api is trying to parse 
at this point I can give you more information.

I am not sure but I am guessing that some of your problems come from 
editing an ontology with a text editor.  We all do this but it is a 
dangerous practice.

-Timothy


On 11/22/2010 06:06 AM, tingyu li wrote:
>
> OK. Lst's forget the problems above, and I have simplified the 
> questions. a new owl files (newversion.owl) has been created, and it 
> can be processed by the codes below, and So does the 
> familyCopy_changed.owl :
>
>     String uri = "file:///C://Users//Li//ontologies//newversion.owl";
>
>
>             OWLModel owlModel = ProtegeOWL.createJenaOWLModelFromURI(uri);
>
>             Collection classes = owlModel.getUserDefinedOWLNamedClasses();
>             //OWLNamedClass destinationClass =
>     owlModel.getOWLNamedClass("family");
>             for (Iterator it = classes.iterator(); it.hasNext();) {
>                 OWLNamedClass cls = (OWLNamedClass) it.next();
>                 Collection instances = cls.getInstances(false);
>                 System.out.println("Class " + cls.getBrowserText() + "
>     (" + instances.size() + ")");
>                 for (Iterator jt = instances.iterator(); jt.hasNext();) {
>                     OWLIndividual individual = (OWLIndividual) jt.next();
>                     System.out.println(" - " +
>     individual.getBrowserText());
>                 }
>             }
>
>  but it can't be processed by the codes PropertyValuee.java, as the 
> same time family.owl can be. I'm so confused by this.  does anybody 
> give me a hint? And the error code is :
>
>     detailed logs:
>     --------------------------------------------------------------------------------
>     Parser: RDFXMLParser
>     org.xml.sax.SAXParseException: The value of attribute
>     "rdf:resource" associated with an element type "rdfs:subClassOf"
>     must not contain the '<' character.
>
>     --------------------------------------------------------------------------------
>     Parser: OWLXMLParser
>     Attribute not found: IRI (Line 30)
>
>     --------------------------------------------------------------------------------
>     Parser: OWLFunctionalSyntaxOWLParser
>     Encountered " <ERROR> "< "" 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.ParseException: Encountered "<!DOCTYPE
>     rdf" at line 4, column 1.
>     Was expecting:
>         "\n" ...
>          (Line 1)
>
>     --------------------------------------------------------------------------------
>     Parser: KRSS2OWLParser
>     de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered
>     "<?xml version=\"1.0\"?>" at line 1, column 1.
>     Was expecting:
>     <EOF>
>
>
>     --------------------------------------------------------------------------------
>     Parser: ManchesterOWLSyntaxOntologyParser
>     Encountered '<?xml version="1.0"?>' 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:619)
>         at
>     uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:585)
>         at
>     uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:589)
>         at
>     com.demo.application.PropertyValuee.main(PropertyValuee.java:26)
>
>
>
>
>
> -- 
> Li
>
>
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