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[protege-discussion] reasoner issue

Tania Tudorache tudorache at stanford.edu
Thu Jun 2 15:07:14 PDT 2011


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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