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Tania Tudorache | 1 May 2008 01:15
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Re: Exception after load ontology from plugin

Hi Esther,

The error indicates that something is wrong with the pprj file. Did you 
override the method:

public String getProjectFilePath() in your KnowledgeBaseFactory?

Does it return null? Or does it return anything else? It should rather 
return null, than point to an invalid pprj file.

It seems that it cannot find the class "PROJECT" in the internal 
knowledgebase, whose singleton instance should describe the form 
configurations.

In the next beta release, the fix up of the project files with old forms 
(where you got the error), will be completely different. So you may not 
get this error, but you may get problems in other parts of the code, if 
the project file is corrupt.

It's hard to tell you more without seeing the code.

Tania

Esther Lozano Hontecillas wrote:
> Hi all,
>
> We've developed a backend plugin that gets the ontology from a database (load and store processes). The
database needs to be updated after every change, so that's why we chose a backend. The plugin consists of 3
classes (one of them extends KnowledgeBaseFactory) that we put DIRECTLY into the protege-owl.jar file
from the protege-owl plugin. We're modified the manifest of this file too by adding the lines:
(Continue reading)

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Tania Tudorache | 1 May 2008 01:17
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Re: need a help

It looks like your owl file is corrupt. Can you send it to us to 
diagnose the problem?

Thanks,
Tania

Khadija Tahera wrote:
> hi
>  
> I was working perfectly with my project suddenly i am getting this 
> following error.
>  
> can anybody please help me? why I am getting this errors?
>  
> Best regards
>  
> Bely
>  
>  
>  
> 2008.04.29 12:42:59.252 BST INFO: ... Loading completed after 1181 ms 
> -- ProtegeOWLParser.loadTriples()
> 2008.04.29 12:42:59.283 BST SEVERE: Error at loading file 
> file:/C:/Program%20Files/Protege_3.3.1/spacecraftprojectfile.owl -- 
> java.lang.ClassCastException: java.lang.String
>  at 
>
edu.stanford.smi.protegex.owl.model.classdisplay.AbstractOWLClassDisplay.getDisplayTextOfOWLNAryLogicalClass(Unknown 
> Source)
>  at
(Continue reading)

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Jennifer Vendetti | 1 May 2008 01:23
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Re: GrOWL

I used Protege 3.4 beta, build 130.  The only other thing I would suggest is to check what version of the JDK you are using.  Protege requires 1.5, and I don't know what GrOWL requires.  You might ask the plug-in developer about this.

Jennifer

cld wrote:
Yes, it is the same plugin I downloaded. What version of protege did you use? I tried to use the plugin to visualize the pizza example using Protege3.4beta but I wasn't enable to see anything. The same error appears. Thanks jvendetti wrote:
I downloaded this plug-in (from this URL: http://www.uvm.edu/~skrivov/growl/org.ecoinformatics.seek.growl.zip, on this page: http://www.uvm.edu/~skrivov/growl/). I was able to bring it up in the user interface and use it to visualize the pizza example ontology. Maybe you are using an older version of Protege and/or this plug-in? Anyway, it's unlikely that the authors of this plug-in monitor the Protege mailing lists. If you continue to have problems, you should try contacting them directly (also check if there are any error messages in the console window and include them with your message). In looking at their Web site, they list this person as the contact: skrivov at zoo.uvm.edu. Jennifer cld wrote:
Hi, I am trying to use the GrOWL View Tab. I have downloaded GrOWL from the website and followed the directions found there: "Unzip the content of the archive into your Plugin directory of your Protégé installation. To use : open your project, select menu item Project | Configure, find GrOWL View on the list and check it". But when I open the GrOWL View Tab the flollowing message appears: "Error loading OWL file". What I am doing wrong? Do I need to do something else to make it work? Thanks in advance
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Ralf Weinand | 1 May 2008 01:28
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Re: How to get rid of the automated dummy.owl processing?

Hi Tanja,

I am excited but also getting a little nervous about the statement
"the processing of imports will be completely different".
Will my code still work? It is based on methods like:
- ProtegeOWL.createOWLJenaModelFromStream(...)
- ImportHelper.importOntologies()
- owlModel.getDefaultOWLOntology().addImports(ontologyName)
- etc
Do you change any interfaces or deprecate methods, so I have to adapt
my program?
When will the next beta be released about?

Cheers,
Ralf

On Thu, May 1, 2008 at 12:21 AM, Tania Tudorache <tudorache <at> stanford.edu> wrote:
> Hi Martin,
>
>  In the next Protege beta, the processing of imports will be completely
>  different. There will be no more "dummy" involved :)
>
>  Tania
>
>
>
>  Martin Winkler wrote:
>  > The dummy.owl processing is only done when one of the imported
>  > ontologies cannot be found. As I meanwhile solved the problem of
>  > imported ontologies (that where not found by the program) I got rid of
>  > the automated dummy.owl loading process.
>  >
>  > ------------------------------------------------------------------------
>  > *Von:* User support for the Protege-OWL editor
>  > *Gesendet:* 30.04.08 09:06:46
>  > *An:* protege-owl <at> lists.stanford.edu
>  > *Betreff:* [protege-owl] How to get rid of the automated dummy.owl
>  > processing?
>  >
>  > This seems to be a well known problem:
>  >
>  > Everytime I start my application from within eclipse, an exception is
>  > thrown during the star tup phase and the stack trace is printed out to
>  > the console. I saw in the mailing list entries that others had the
>  > same problem but I found no answered entry. (maybe my evil ms browser
>  > hides them :) I don't want to defy the etiquette, just can't find the
>  > answer.
>  >
>  > The exception is caused by the startup activity 'Start processing
>  > ontology: http://dummy-ontologies.com/dummy.owl'
>  > <http://dummy-ontologies.com/dummy.owl%27>
>
> >
>  >
>  >
>  > In 5 Schritten zur eigenen Homepage. Jetzt Domain sichern und
>  > gestalten!
>  > Nur 3,99 EUR/Monat! *http://www.maildomain.web.de/?mc=021114*
>  >
>  > ------------------------------------------------------------------------
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>  > listprotege-owl <at> lists.sta
>  > nford.eduhttps://mailman.stanford.edu/mailman/listinfo/protege-owlInstructions
>  > for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>  >
>  >
>  >
>  >
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>  > Homepage mit eigenem Namen. Jetzt starten!
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Tania Tudorache | 1 May 2008 01:38
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Re: Importing several ontologies from stream

Hi Ralf,

I have made the setErrorLevel public. The parser code in the next beta 
release will be much different than the one in the current release. 
Please remind me to post an example for importing from streams after we 
release the new beta.

Thanks,
Tania

Ralf Weinand wrote:
> Hi Tania,
>
> thanks a lot for this hint!
> No it works without temp files and repositories! Great!
>
> The methods
> - createARPInvokation(final Reader reader, final String uri)
> - setErrorLevel(ARP arp)
> are not public so I had to copy them into my class.
> maybe you could make them public?
>
> Anyway, thanks heaps again!
>
> Ralf
>
>
>
>
> On Thu, Apr 24, 2008 at 1:51 AM, Tania Tudorache <tudorache <at> stanford.edu> wrote:
>   
>> Ralf,
>>
>>  You can do the import from a stream, but not in a straightforward way. Look
>> at the method:
>>
>>  public static void addImport(JenaOWLModel owlModel,
>>                                 URI ontologyName,
>>                                 String prefixForDefaultNamespace)
>>
>>  from ProtegeOWLParser.java (I've attached the class code). You can
>> basically copy that code in your own method. Make sure that you also add the
>> import statement to the importing ontology (see javadoc comment) after you
>> do the import. Probably you can get rid of the repository code in the
>> method.
>>
>>  Tania
>>
>>
>>
>>
>>
>>  Ralf Weinand wrote:
>>
>>     
>>> Hi Tania,
>>>
>>> thanks for the hint.
>>> I don´t think, that this method is what I need, but I did see another
>>> (undocumented) method in RepositoryUtil:
>>>
>>>       
>> http://protege.stanford.edu/download/prerelease_javadoc_owl/edu/stanford/smi/protegex/owl/repository/util/RepositoryUtil.html#createImportLocalCopy(edu.stanford.smi.protegex.owl.model.OWLModel,%20java.net.URI,%20java.io.File)
>>     
>>> Can you tell me what it does?
>>>
>>> Again my problem: i don´t have these ontologies stored physically.
>>> I receive them as org.w3c.dom.Element objects so I do not have a
>>> physical location (URL).
>>> They are just in memory, but I have to import them into one common
>>> knowledgebase.
>>> That´s why I have to write them temporarily to files and them load the
>>> first one and import the others.
>>> I´m looking for a better approach.
>>>
>>> Thanks!
>>> Ralf
>>>
>>>
>>>
>>> On Wed, Apr 23, 2008 at 3:36 AM, Tania Tudorache <tudorache <at> stanford.edu>
>>>       
>> wrote:
>>     
>>>       
>>>> Ralf,
>>>>
>>>>  There was recently a post that might be relevant. See this thread [1].
>>>>
>>>>  There is a new utility method,
>>>>  RepositoryUtil.loadProjectRepositoriesFromURI(...) that may help. See
>>>>  also the Javadoc of this method. You can add as a project repository a
>>>>  URL and then do the import with the ontology name (not ontology URL).
>>>>  The parser will look at the repositories and get an input stream from
>>>>  the repository URL.
>>>>
>>>>  I haven't tested this yet, but I think it should work.
>>>>
>>>>  Tania
>>>>
>>>>  [1]:
>>>>         
>> http://article.gmane.org/gmane.comp.misc.ontology.protege.owl/24368
>>     
>>>>
>>>>
>>>>  Ralf Weinand wrote:
>>>>  > Hi,
>>>>  >
>>>>  > I am writing a program that receives several ontologies (as strings -
>>>>  > or, to be more precise - as RDF/XML serializations).
>>>>  > All of these ontologies have to be imported into one common knowledge
>>>>  > base to perform some reasoning (also using Jess for SWRL rules).
>>>>  > Now I am facing a problem. The first serialization I can simply load
>>>>         
>> via
>>     
>>>>  >
>>>>  >             dataflowModel =
>>>>  > ProtegeOWL.createJenaOWLModelFromReader(new StringReader(ontology1));
>>>>  >
>>>>  > But for the rest of the ontologies I have to first write each one
>>>>         
>> into
>>     
>>>>  > a temporary file, take the URI and use this URI
>>>>  > to import the ontology via
>>>>  >
>>>>  >             ImportHelper importHelper = new
>>>>         
>> ImportHelper(dataflowModel);
>>     
>>>>  >
>>>>  >             for (int i = 3; i < aArgs.size(); i++)
>>>>  >             {
>>>>  >                 File sourceModelFile =
>>>>  > SemanticUtils.writeOntologyToTempFile(aArgs.get(i));
>>>>  >                 importHelper.addImport(sourceModelFile.toURI());
>>>>  >             }
>>>>  >
>>>>  >             importHelper.importOntologies();
>>>>  >
>>>>  > Isn´t there a mode convenient method to do this?
>>>>  > I don´t like the idea of using temp-files.
>>>>  >
>>>>  > Also, I am facing some problems with this method (some dependencies
>>>>  > regarding the order in which I do the imports).
>>>>  > Do I have to use a repository manager somehow?
>>>>  > Any recommendations?
>>>>  >
>>>>  > Cheers,
>>>>  > Ralf
>>>>  > _______________________________________________
>>>>  > 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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>>>>
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>>>>         
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>>     
>>>>
>>>>         
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>>     
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Tania Tudorache | 1 May 2008 01:59
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Re: how to convert owl to uml?

Leila,

There are several visualization plugins in Protege. You could try OWLViz 
[1] or Jambalaya [2]. If this is the only reason why you converted to 
UML, then your problem is solved :)

However, if you need the UML for different reasons, then, yes, you need 
a UML tool to visualize the UML diagram. There are several ones 
available (e.g. Poseidon for UML [3]).

Tania

[1]: http://protegewiki.stanford.edu/index.php/OWLViz
[2]: http://protegewiki.stanford.edu/index.php/Jambalaya
[3]: http://www.gentleware.com/

LEILA ZEMMOUCHI wrote:
> Hello,
>
> I want to transform owl ontologies to uml class diagrams, i've already 
> convert these ontologies to format uml 1.4, i've obtained .xmi files, 
> but how to vizulalize them as class diagrams, is it feasible under 
> protégé platform or i have to search about an uml tool for this request.
>
> Regards,
>
> Mrs Ghomari Leila,
> A Research Master Student,
> INI (National Institute of Computer Science), Algiers, Algeria.
>
> __________________________________________________
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Tania Tudorache | 1 May 2008 02:32
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Re: How to get rid of the automated dummy.owl processing?

Hi Ralf,

The new beta release (which is already in SVN, in case you want to try 
it out), will come out very soon (was planned for this week, but it may 
be next week).

This will be a major release containing a reimplementation of the parser 
and naming mechanism, and also the database inclusion. We have tried to 
keep all interface methods the same, and to deprecate the ones that are 
not recommended anymore. So mostly, the implementation has changed, not 
the interfaces.

The ImportHelper will work the same way, and also the other methods that 
you mentioned. Some code that uses directly the classes, rather than the 
interfaces, may need to change slightly, but we try to minimize that. 
Probably your code for importing from stream will get simplified, as we 
will be able to support that in a more natural way.

Tania

Ralf Weinand wrote:
> Hi Tanja,
>
> I am excited but also getting a little nervous about the statement
> "the processing of imports will be completely different".
> Will my code still work? It is based on methods like:
> - ProtegeOWL.createOWLJenaModelFromStream(...)
> - ImportHelper.importOntologies()
> - owlModel.getDefaultOWLOntology().addImports(ontologyName)
> - etc
> Do you change any interfaces or deprecate methods, so I have to adapt
> my program?
> When will the next beta be released about?
>
> Cheers,
> Ralf
>
>
> On Thu, May 1, 2008 at 12:21 AM, Tania Tudorache <tudorache <at> stanford.edu> wrote:
>   
>> Hi Martin,
>>
>>  In the next Protege beta, the processing of imports will be completely
>>  different. There will be no more "dummy" involved :)
>>
>>  Tania
>>
>>
>>
>>  Martin Winkler wrote:
>>  > The dummy.owl processing is only done when one of the imported
>>  > ontologies cannot be found. As I meanwhile solved the problem of
>>  > imported ontologies (that where not found by the program) I got rid of
>>  > the automated dummy.owl loading process.
>>  >
>>  > ------------------------------------------------------------------------
>>  > *Von:* User support for the Protege-OWL editor
>>  > *Gesendet:* 30.04.08 09:06:46
>>  > *An:* protege-owl <at> lists.stanford.edu
>>  > *Betreff:* [protege-owl] How to get rid of the automated dummy.owl
>>  > processing?
>>  >
>>  > This seems to be a well known problem:
>>  >
>>  > Everytime I start my application from within eclipse, an exception is
>>  > thrown during the star tup phase and the stack trace is printed out to
>>  > the console. I saw in the mailing list entries that others had the
>>  > same problem but I found no answered entry. (maybe my evil ms browser
>>  > hides them :) I don't want to defy the etiquette, just can't find the
>>  > answer.
>>  >
>>  > The exception is caused by the startup activity 'Start processing
>>  > ontology: http://dummy-ontologies.com/dummy.owl'
>>  > <http://dummy-ontologies.com/dummy.owl%27>
>>
>>     
>>  >
>>  >
>>  > In 5 Schritten zur eigenen Homepage. Jetzt Domain sichern und
>>  > gestalten!
>>  > Nur 3,99 EUR/Monat! *http://www.maildomain.web.de/?mc=021114*
>>  >
>>  > ------------------------------------------------------------------------
>>  > _______________________________________________protege-owl mailing
>>  > listprotege-owl <at> lists.sta
>>  > nford.eduhttps://mailman.stanford.edu/mailman/listinfo/protege-owlInstructions
>>  > for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>>  >
>>  >
>>  >
>>  >
>>  > EINE FÜR ALLE: die kostenlose WEB.DE-Plattform für Freunde und Deine
>>  > Homepage mit eigenem Namen. Jetzt starten!
>>  > *http://unddu.de/?kid=kid <at> mf2*
>>  >
>>  > ------------------------------------------------------------------------
>>  >
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>>  > protege-owl mailing list
>>  > protege-owl <at> lists.stanford.edu
>>
>>     
>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>       
>>  >
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Tania Tudorache | 1 May 2008 03:02
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Re: Problem with ProtegeReasoner.getIndividualsBelongingToClass(OWLClass) method

Interesting. I've just did a test and it actually returned the inferred 
individuals of an intersection.

I used your example, and got the union class from the range of a 
property. Then, I asked for the individuals belonging to that union and 
it returned the expected results.

This should work in the latest beta (build 130). I suppose this is what 
you used, too.

If you still have problems with this, can you please send me the 
ontology that has this behavior, and write me also exactly for what 
union class you were trying to get the individuals.

Thanks,
Tania

Mariusz Gwiazda wrote:
> Dear All,
>
> I'm using 
> ProtegePelletJenaReasoner.getIndividualsBelongingToClass(OWLClass) 
> method to get all individuals that belong to the range of property. In 
> my ontology ranges of properties are OWLNamedClass or union of this kind 
> of classes. I'm getting property range as OWLClass on this way:
>
> RDFResource range = property.getRange(true);
> OWLClass cls = (OWLClass) range;
>
> If cls object is exactly object of OWLNamedClass, method returns 
> appropriate individuals. Problem starts when I pass to this method 
> OWLUnionClass object (simple union of OWLNamedClass), it returns 
> nothing. It happens also for OWLIntersectionClass.
>
> It is a bug?
>
> For now, I write some workaround. I get all operands of OWLUnionClass 
> and for each operand I invoke getIndividualsBelongingToClass method, but 
> this is not universal solution.
>
>
> Best wishes,
> Mariusz
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kiran dasari | 1 May 2008 07:16
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SPARQL - OWL

Hi,

I can't get this code to work. Can someone have a look at it.

String queryString = "PREFIX pf:<http://www.owl-ontologies.com/unnamed.owl#>" +
                                "SELECT ?Sensor" +
                                "FROM<http://www.owl-ontologies.com/unnamed.owl>" +
                                "WHERE{?Sensor pf:hasSensorID "+ 100 +"}";
The error is
com.hp.hpl.jena.query.QueryParseException: Encountered "<http://www.owl-ontologies.com/unnamed.owl>"
Was expecting one of:
<VAR1> ...
    <VAR2> ...
    "from" ...
    "where" ...
    "{" ...


Thanks,
Kiran 

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drazik | 1 May 2008 12:58
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SQWRL


hi all
I have a problem whith this query :
tbox:isSubClassOf (?subclass, Permission) -> sqwrl:select(?subclass)
when I write this query in protege 3.4beta and I run it I get any result!!!

where is the problem? please 
thanks
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Gmane