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[protege-discussion] inconsistent ontology error

Timothy Redmond tredmond at stanford.edu
Mon Jun 27 17:37:04 PDT 2011


I also classified the ontology with HermiT and with Pellet without an 
inconsistency.

My first guess would be to agree with Tania that the issue is probably 
with the imports.  The thing in your message that needs explaining is 
why the pellet command line would behave differently than pellet within 
Protege.  My guess is that the difference comes because Protege probably 
loads imports differently than pellet.  Protege tries to load imports 
from the local drive first.  Pellet probably goes to the internet first.

There are other differences perhaps.  A version difference (pellet 2.1.2 
is the latest in Protege but this is different than 2.2.1??).  Or 
perhaps a difference with how the ontology is loaded (Protege uses the 
OWL api - I wonder what the pellet command line uses?).

Did you have some of the imports on your disk?  You could remove this 
issue by creating a merged version of your ontology (Refactor->Merge 
ontologies...).

> In case you do get the inconsistent ontology error again, please go to 
> the Reasoner menu -> Explain inconsistent ontology and see which 
> statements are likely to cause this error.

This explanation tool is pretty limited - the pellet command line is better.

-Timothy



On 06/27/2011 04:38 PM, Tania Tudorache wrote:
> Hi Jie,
>
> I just tried out in the latest Protege 4.1 release candidate (build 
> 231) the ontology you sent with Pellet 2.1.2, and it classified 
> without any problem. It took a little bit of time, though.
>
> I noticed that some of the imports are not always available online. I 
> wonder if the inconsistent ontology error is somehow caused by this 
> (although you would not expect it).
>
> In case you do get the inconsistent ontology error again, please go to 
> the Reasoner menu -> Explain inconsistent ontology and see which 
> statements are likely to cause this error.
>
> Tania
>
>
> On 06/27/2011 04:05 PM, Jie Zheng wrote:
>> Hi,
>>
>> I worked on an ontology. When I ran reasoners (HermiT 1.3.4 and 
>> Pellet 2.2.1) in Protege 4.1, both gave me inconsistent ontology 
>> error. However, I ran Pellet 2.2.1 from command line . The result 
>> shows ontology is consistent. I also tried to use latest stable 
>> HermiT (jar downloaded on June 7, 2011) call from OWL API. It also 
>> show no unsatisfied classes and can display the classes in the 
>> inferred hierarchy. I cannot figure out why. I attached the owl for 
>> check.
>>
>> Any help would be appreciated.
>>
>> Jie
>>
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