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[protege-discussion] inconsistent ontology error

jie zheng jiezheng at pcbi.upenn.edu
Mon Jun 27 19:00:54 PDT 2011


Hi Timothy,

I got import error when I ran Pellet 2.2.1 using command line. However, 
I still got ontology consistent message.

It is weird if the error caused by imports. The OWL file I attached with 
changes we made based on the other OWL file which is consistent and I 
reasoned it again after I got problem with the changed version.

I will try again tomorrow to see whether I can reproduce the errors.

Thanks for your help.

Jie


On 6/27/2011 8:37 PM, Timothy Redmond wrote:
>
> 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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