[protege-owl] unable to OWL-RDF load model after quitting protege

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[protege-owl] unable to OWL-RDF load model after quitting protege

Nikolaj Berntsen
Dear Protege-owl users.

I have created a model from scratch with protege (trying to get more
clean-cut trouble than in my earlier posts). After saving and quitting I
have three files saved:

foo.rdf-xml.repository
foo.rdf-xml.owl
foo.pprj

The model I create has a tree structure of classes, some disjoint
(created thru the wizard for multiple classes), some not, some data type
properties and some object properties as well as a value partition type
(created from the patterns menu).

When I clivk the pprj file I get the following exception [1]. I have had
no exceptions when creating the file, only some warnings
    WARNING: Invalid frame type: SimpleInstance
when creating two instances.

I run protege-own 2.2 build 311 in protege 3.1 build 318.


Hope someone can give me some clues, as I would really like to be able
to use this fine tool.

/\/

[1]
java.lang.ClassCastException:
edu.stanford.smi.protegex.owl.model.impl.DefaultOWLIntersectionClass
    at
edu.stanford.smi.protegex.owl.model.impl.DefaultRDFList.getRest(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.model.impl.DefaultRDFList.getValues(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.model.impl.AbstractOWLNAryLogicalClass.getOperands(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.RDFPropertyPostProcessor.updateValueType(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.RDFPropertyPostProcessor.<init>(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.TripleChangePostProcessor.postProcess(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStoreModel.endTripleStoreChanges(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
Source)
    at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(Unknown Source)
    at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(Unknown Source)
    at
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(Unknown
Source)
    at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown Source)
    at
edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown
Source)
    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
    at edu.stanford.smi.protege.model.Project.loadProjectFromURI(Unknown
Source)
    at
edu.stanford.smi.protege.ui.ProjectManager.loadProjectFromURI(Unknown
Source)
    at edu.stanford.smi.protege.ui.ProjectManager.loadProject(Unknown
Source)
    at edu.stanford.smi.protege.Application.init(Unknown Source)
    at edu.stanford.smi.protege.Application.realmain(Unknown Source)
    at edu.stanford.smi.protege.Application$3.run(Unknown Source)

Please consider running the file through an RDF or OWL validation
service such as
  - RDF Validator: http://www.w3.org/RDF/Validator
  - OWL Validator: http://phoebus.cs.man.ac.uk:9999/OWL/Validator

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[protege-owl] Re: unable to OWL-RDF load model after quitting protege

Nikolaj Berntsen
I found a way (a FAQ way, even, blush) to load my file
    http://protege.stanford.edu/plugins/owl/protege-owl-faq.html
see the section on "How can I load an OWL File?".

As my bug arose when trying to load the pprj file, I think my question
stands (at least why do you create pprj files when they cannot load again).

Further, when I succeed to load the file as described in the FAQ my
protege does not show the OWL menu any more.... Sorry if I ask too many
questions answered on the website, but I guess that is the punishement
for making clicky clicky tools available to the general public :-(

Till next time,
/\/

Nikolaj Berntsen wrote:

>Dear Protege-owl users.
>
>I have created a model from scratch with protege (trying to get more
>clean-cut trouble than in my earlier posts). After saving and quitting I
>have three files saved:
>
>foo.rdf-xml.repository
>foo.rdf-xml.owl
>foo.pprj
>
>The model I create has a tree structure of classes, some disjoint
>(created thru the wizard for multiple classes), some not, some data type
>properties and some object properties as well as a value partition type
>(created from the patterns menu).
>
>When I clivk the pprj file I get the following exception [1]. I have had
>no exceptions when creating the file, only some warnings
>    WARNING: Invalid frame type: SimpleInstance
>when creating two instances.
>
>I run protege-own 2.2 build 311 in protege 3.1 build 318.
>
>
>Hope someone can give me some clues, as I would really like to be able
>to use this fine tool.
>
>/\/
>
>[1]
>java.lang.ClassCastException:
>edu.stanford.smi.protegex.owl.model.impl.DefaultOWLIntersectionClass
>    at
>edu.stanford.smi.protegex.owl.model.impl.DefaultRDFList.getRest(Unknown
>Source)
>    at
>edu.stanford.smi.protegex.owl.model.impl.DefaultRDFList.getValues(Unknown
>Source)
>    at
>edu.stanford.smi.protegex.owl.model.impl.AbstractOWLNAryLogicalClass.getOperands(Unknown
>Source)
>    at
>edu.stanford.smi.protegex.owl.model.triplestore.impl.RDFPropertyPostProcessor.updateValueType(Unknown
>Source)
>    at
>edu.stanford.smi.protegex.owl.model.triplestore.impl.RDFPropertyPostProcessor.<init>(Unknown
>Source)
>    at
>edu.stanford.smi.protegex.owl.model.triplestore.impl.TripleChangePostProcessor.postProcess(Unknown
>Source)
>    at
>edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStoreModel.endTripleStoreChanges(Unknown
>Source)
>    at
>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(Unknown
>Source)
>    at
>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
>Source)
>    at
>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
>Source)
>    at
>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
>Source)
>    at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(Unknown Source)
>    at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(Unknown Source)
>    at
>edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(Unknown
>Source)
>    at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown Source)
>    at
>edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown
>Source)
>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>    at edu.stanford.smi.protege.model.Project.loadProjectFromURI(Unknown
>Source)
>    at
>edu.stanford.smi.protege.ui.ProjectManager.loadProjectFromURI(Unknown
>Source)
>    at edu.stanford.smi.protege.ui.ProjectManager.loadProject(Unknown
>Source)
>    at edu.stanford.smi.protege.Application.init(Unknown Source)
>    at edu.stanford.smi.protege.Application.realmain(Unknown Source)
>    at edu.stanford.smi.protege.Application$3.run(Unknown Source)
>
>Please consider running the file through an RDF or OWL validation
>service such as
>  - RDF Validator: http://www.w3.org/RDF/Validator
>  - OWL Validator: http://phoebus.cs.man.ac.uk:9999/OWL/Validator
>
>-------------------------------------------------------------------------
>To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>
>
>  
>


--
Cheers,
/\/ikolaj Berntsen
--
Mobile People A/S
Toldbodgade 31, 2 sal, DK-1253 Copenhagen K
T: +45 7025 2722 F: 70 25 27 23 M: +45 3054 2207

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[protege-owl] Re: unable to OWL-RDF load model after quitting protege

Tania Tudorache
Nikolaj,

see my answers inline.

Tania

Nikolaj Berntsen wrote:

>I found a way (a FAQ way, even, blush) to load my file
>    http://protege.stanford.edu/plugins/owl/protege-owl-faq.html
>see the section on "How can I load an OWL File?".
>
>  
>
It seems you are using the latest Protege 3.2 beta 318, so you don't
need to go through the "New project" -> "Create from existing sources"
step. This was necessary for the Protege release version (3.1 and
3.1.1).  In your version, you can simply choose the owl file from the
"Open.." menu.

>As my bug arose when trying to load the pprj file, I think my question
>stands (at least why do you create pprj files when they cannot load again).
>  
>
I suspect that: either there is something wrong with your Protege
installation (for example, did you move the Protege installation
directory after install?) or something went wrong when saving the pprj
file, especially cause you got warnings. Try opening the owl file, not
the pprj file. Start Protege, "File"->"Open.." -> select the owl file.

>Further, when I succeed to load the file as described in the FAQ my
>protege does not show the OWL menu any more.... Sorry if I ask too many
>questions answered on the website, but I guess that is the punishement
>for making clicky clicky tools available to the general public :-(
>
>  
>
Same answer as before. If opening the owl file does not work, then
please validate the OWL file
(http://phoebus.cs.man.ac.uk:9999/OWL/Validator) and if it is valid,
send it to me to see what went wrong.

Tania



>Till next time,
>/\/
>
>Nikolaj Berntsen wrote:
>
>  
>
>>Dear Protege-owl users.
>>
>>I have created a model from scratch with protege (trying to get more
>>clean-cut trouble than in my earlier posts). After saving and quitting I
>>have three files saved:
>>
>>foo.rdf-xml.repository
>>foo.rdf-xml.owl
>>foo.pprj
>>
>>The model I create has a tree structure of classes, some disjoint
>>(created thru the wizard for multiple classes), some not, some data type
>>properties and some object properties as well as a value partition type
>>(created from the patterns menu).
>>
>>When I clivk the pprj file I get the following exception [1]. I have had
>>no exceptions when creating the file, only some warnings
>>   WARNING: Invalid frame type: SimpleInstance
>>when creating two instances.
>>
>>I run protege-own 2.2 build 311 in protege 3.1 build 318.
>>
>>
>>Hope someone can give me some clues, as I would really like to be able
>>to use this fine tool.
>>
>>/\/
>>
>>[1]
>>java.lang.ClassCastException:
>>edu.stanford.smi.protegex.owl.model.impl.DefaultOWLIntersectionClass
>>   at
>>edu.stanford.smi.protegex.owl.model.impl.DefaultRDFList.getRest(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protegex.owl.model.impl.DefaultRDFList.getValues(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protegex.owl.model.impl.AbstractOWLNAryLogicalClass.getOperands(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protegex.owl.model.triplestore.impl.RDFPropertyPostProcessor.updateValueType(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protegex.owl.model.triplestore.impl.RDFPropertyPostProcessor.<init>(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protegex.owl.model.triplestore.impl.TripleChangePostProcessor.postProcess(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStoreModel.endTripleStoreChanges(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
>>Source)
>>   at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(Unknown Source)
>>   at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(Unknown Source)
>>   at
>>edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(Unknown
>>Source)
>>   at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown Source)
>>   at
>>edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown
>>Source)
>>   at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>>   at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>>   at edu.stanford.smi.protege.model.Project.loadProjectFromURI(Unknown
>>Source)
>>   at
>>edu.stanford.smi.protege.ui.ProjectManager.loadProjectFromURI(Unknown
>>Source)
>>   at edu.stanford.smi.protege.ui.ProjectManager.loadProject(Unknown
>>Source)
>>   at edu.stanford.smi.protege.Application.init(Unknown Source)
>>   at edu.stanford.smi.protege.Application.realmain(Unknown Source)
>>   at edu.stanford.smi.protege.Application$3.run(Unknown Source)
>>
>>Please consider running the file through an RDF or OWL validation
>>service such as
>> - RDF Validator: http://www.w3.org/RDF/Validator
>> - OWL Validator: http://phoebus.cs.man.ac.uk:9999/OWL/Validator
>>
>>
>>
>>    
>>
>
>
>  
>

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[protege-owl] Re: unable to OWL-RDF load model after quitting protege

Nikolaj Berntsen
Tania,

> It seems you are using the latest Protege 3.2 beta 318, so you don't
> need to go through the "New project" -> "Create from existing sources"
> step. This was necessary for the Protege release version (3.1 and
> 3.1.1).  In your version, you can simply choose the owl file from the
> "Open.." menu.

Did not occur to me, tried it just now, works like a charm.

I see a single warning in the console:

[ProtegeUI]  Warning: No ProjectView registered for project
foo-exported.rdf-xml

I think the warnings comes after:
    new project
    import from sources, choosing the owl file
    now in protege without an OWL menu
    export to format > OWL

but that seems to not cause any trouble presently.

> I suspect that: either there is something wrong with your Protege
> installation (for example, did you move the Protege installation
> directory after install?) or something went wrong when saving the pprj
> file, especially cause you got warnings. Try opening the owl file, not
> the pprj file. Start Protege, "File"->"Open.." -> select the owl file.

I did not move my protege installation. I think I chose all default
values (with a placement in C:\Program Files\Protege.........), perhaps
the space is bothering protege? (IMO spaces in file and directory name
should be depracated, but that is my windows installation default).
As I reported above, directly opening the OWL file works like a charm, I
end up in protege with OWL menus available.

> Same answer as before. If opening the owl file does not work, then
> please validate the OWL file
> (http://phoebus.cs.man.ac.uk:9999/OWL/Validator) and if it is valid,
> send it to me to see what went wrong.

I checked the validity before, when I read the FAQ, and everything
summed up nicely.

By the way, what is the recommendation for OWL dialect, when I
    don't plan on much automatic deduction/reasoning on the datamodel
    plan to export RDF with lotsa RDF:Description on classes with my own
properties?

I am a bit confused about what kind of naming convention I should use
for my properties (verbs)? In
http://www.co-ode.org/resources/tutorials/ProtegeOWLTutorial.pdf (I
think it was) they recommend using either of the forms:
is.... has..... for some reason (something to do with generating english
descriptions of the ontology). Eventually I hope to export my OWL
ontology to EMF interfaces and generate an implementation. For this
reason, I wonder if the proper thing for me is to have nouns as
properties, since the generated methods otherwise will have names such
as "getIsFoo" and "getHasBar" which seems a bit confused to me? Do you
have an opinnion on that?

Cheers,
/\/




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