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[protege-discussion] inconsistent ontology error
jiezheng at pcbi.upenn.edu
Tue Jun 28 08:53:00 PDT 2011
I tried today. Still got inconsistent ontology error message even after
I created a merge ontology using Protege 'merge ontologies ...'.
However, the reasoning on the file you sent to me works fine.
I remembered I had this problem before. But after I restart the computer
it is gone away. It did not happen this time. I will try again in the
future. Since the ontology is consistent, we can go ahead to work on
Thanks a lot for your help.
On 6/28/2011 11:32 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.
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