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[protege-discussion] oversized file

Timothy Redmond tredmond at
Tue Jun 28 10:02:36 PDT 2011

Sorry for sending such an over-sized file - I didn't realize it was so 
big when it went out...


On 06/28/2011 08:32 AM, Timothy Redmond wrote:
> I think that the thing to explain is why the experiments are not 
> repeatable.  Why haven't I seen the inconsistency when I classify your 
> ontology?  (I have now classified it several times with different 
> reasoners.)  Why did the pellet command line give different results 
> than Protege?
>> Hi Timothy,
>> I got import error when I ran Pellet 2.2.1 using command line. 
>> However, I still got ontology consistent message.
> If you are getting an import error on the command line but not in 
> Protege then this is consistent with the idea that the issue is with 
> the imports.  You are seeing evidence that the imports are run 
> differently from the command line than they are from Protege.
>> It is weird if the error caused by imports.
> A difference with the imported ontologies still seems like the most 
> likely theory to me.  But there are easy things that you can do to 
> rule this out.   Note that I am not necessarily suggesting that either 
> version of the imported ontologies has a problem.  I am just focusing 
> on something that would be different from Protege, the pellet command 
> line and here at Stanford.
> The simplest way to rule out imports is to put your ontology into a 
> new and completely empty directory.  Then Protege and pellet will be 
> forced to find all the imports off the web.   This is not a completely 
> repeatable experiment because the web is an unreliable medium and can 
> provide different results at different times.  But if you do this and 
> the pellet command line and Protege still reach different results you 
> can be 90% certain it is not the imports.
> A better way to make a reproducible experiment would be to merge the 
> ontology and its imports all into one file.  This can be done with the 
> Refactor->Merge Ontologies... menu.  In the select ontologies to merge 
> window you select all the ontologies.  In the select merge type you 
> choose create new ontology.  When you merge it you may have to give 
> the new ontology a different name than the existing ones (I am not 
> sure about this but if it is true then it is a bug that I should fix).
> The result of this is a single merged file with no imports.  The file 
> is then not dependent on any unreliable i/o operations and the results 
> of a load and classify should be consistent.  You should then be able 
> to share this file with others and expect the them to get the same 
> results as you do.  You should expect that the pellet command line 
> will give the same results as Protege.  If this is not so then this is 
> more interesting and we will have to think harder.
> I have attached my version of the merged file that I have now 
> classified with FaCT++ and HermiT without any exceptions.  I will try 
> pellet later today.
>> 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.
> Inference can be delicate.  A very small innocent looking change can 
> make the whole ontology go bad.  In addition you have a small but 
> significant number of individuals in your ontology.  A small fault 
> with individuals can make the ontology inconsistent and render the 
> reasoner useless.  The fact that a change in the imported ontologies 
> leads to a contradiction does not mean that there is a problem with 
> either version of the imported ontologies.
> -Timothy
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