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[protege-discussion] reasoner issue

Jie Zheng jiezheng at pcbi.upenn.edu
Thu Jun 2 15:16:16 PDT 2011


Hi Tania,

Thanks for your explanation.

The reason I checked consistent of the ontology using Protege 3.x 
because we are thinking to use collaborative ontology development tool, 
WebProtégé, which only supported by Protege 3.x.

I have used Protege 3.4.1 before to develop OBI which imports BFO too. 
The Pellet worked fine. It's strange to have this issue now.

Best,

Jie

On 6/2/2011 6:07 PM, Tania Tudorache wrote:
> Hi Jie,
>
> In general, it is better to trust the reasoning capabilities of 
> Protege 4.x rather than Protege 3.x. I checked and your ontology is 
> consistent.
>
> The reason you get the inconsistent classes in Protege 3.x is because 
> of a class cast exception that happens while the ontology is "sent" to 
> the reasoner. The cause for this exception is that the class 
> "http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant" 
> that has as declared types both rdfs:Class and owl:Class in two 
> different imports, and Protege 3.x creates it as a RDFSNamedClass 
> object rather than a OWLNamedClass object, and hence the class cast 
> exception. If the ontology would make it fine to the reasoner in 
> Protege 3.x, it would be consistent.
>
> So, I would suggest that you continue to use Protege 4.1, if possible. 
> We'll add the bug to be fixed for Protege 3.x, but as this is not a 
> very common situation, and the fix would involve some performance hit, 
> we will need to consider it carefully.
>
> Cheers,
> Tania
>
>
> On 06/02/2011 01:55 PM, Jie Zheng wrote:
>> We developed an ontology using Protege 4.1. The Pellet and Hermit 
>> were used for consistent checking and inference. No inconsistency is 
>> found. However, when we ran Pellet 1.5.2 in Protege 3.4.6, it showed 
>> a long list of inconsistent concepts. The following message was shown 
>> when ran the Pellet:
>>
>> WARNING: Errors at synchronizing OWL model with the reasoner -- 
>> java.lang.ClassCastException: 
>> edu.stanford.smi.protegex.owl.model.impl.DefaultRDFSNamedClass can
>> not be cast to edu.stanford.smi.protegex.owl.model.OWLNamedClass
>>         at 
>> edu.stanford.smi.protegex.owl.owlapi.converter.OWLAPIConverter.convertClasses(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.owlapi.converter.OWLAPIConverter.convert(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.inference.pellet.ProtegePelletOWLAPIReasoner.getOwlApiOntology(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.inference.pellet.ProtegePelletOWLAPIReasoner.rebind(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.inference.protegeowl.task.protegereasoner.SynchronizeReasonerTask.transmitToReasoner(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.inference.protegeowl.task.protegereasoner.SynchronizeReasonerTask.run(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.inference.reasoner.AbstractProtegeReasoner.synchronizeReasoner(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.inference.pellet.AbstractProtegePelletReasoner.performTask(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.inference.reasoner.AbstractProtegeReasoner.performTask(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.inference.reasoner.AbstractProtegeReasoner.computeInferredIndividualTypes(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.inference.ui.action.ComputeInferredTypesAction$1.executeReasonerActions(Unknown 
>> Source)
>>         at 
>> edu.stanford.smi.protegex.owl.inference.ui.ReasonerActionRunner$2.run(Unknown 
>> Source)
>>         at java.lang.Thread.run(Unknown Source)
>>
>> We don't know whether the ontology is inconsistent or it is caused by 
>> incompatible of two versions of Protege or some other issues.
>>
>> I attached the ontology. Any help on it is appreciated.
>>
>> Thanks,
>>
>> Jie
>>
>>
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