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[protege-owl] problem loading galen.owl with protege 3 and protege 4

Timothy Redmond tredmond at stanford.edu
Wed Aug 1 09:54:03 PDT 2007


I apologize but my last reply only adressed Protege 4.  I just loaded  
this ontology into Protege 3 also without problems.  In the Protege 3  
case, are you sure there were no exceptions on the console or in the  
logs?  No dialog box popped up?  My suspicion is that you ran out of  
memory in Protege 3 also but I would have thought it would inform you  
of this.

The ontology loads pretty quickly into Protege 4 though there are  
some messages about strange constructs.  In Protege 3  it takes much  
longer.  On the screen I have a log message that says

	INFO: ... Loading completed after 470143 ms

This is over  7 minutes.  Admittedly I am using a slow  machine but  
this is still a long time and the full time from trying to load it to  
display is even longer (I didn't time it).  In Protege 3 of course  
you can consider the database backend if you want quicker loading  
(after the database has been populated.)

-Timothy


On Aug 1, 2007, at 9:28 AM, Timothy Redmond wrote:

>
> You have almost certainly run into an out-of-memory error.
> Unfortunately the logging in Protege 4 still has a bit of a problem
> and the exception is not always displayed.   If you can, increase the
> memory and let us know how it goes.
>
> I believe that I fixed the problem with logging last night on an
> internal development branch (it will find its way to the head).
>
> -Timothy
>
>
> On Aug 1, 2007, at 8:23 AM, helen.chen at agfa.com wrote:
>
>>
>> Dear list
>>
>>
>> I downloaded protege 4 and trying to open a local copy of galen.owl
>> [1].  The owl file is about 21M..  After loading 220,000 triples
>> (message on console), the system hung forever (I have to kill the
>> process after more than 30 minutes waiting).
>>
>> This is the same problem with protege 3.2.
>>
>> Can anyone share his/her experience in loading large ontology in
>> protege?  Is there a place where I can specify a larger memory
>> space for loading large ontology?
>>
>> Thanks.
>>
>> Helen
>>
>> [1] full galen owl ontology http://bioontology.org/projects/
>> ontologies/galen/galen.owl
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