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[protege-owl] Convert a large ontology (e.g. Gene Ontology) to OWL 2 XML

Timothy Redmond tredmond at
Tue Jan 19 08:33:29 PST 2010

Thanks for your information.  I am sorry that I didn't reply earlier.

Christoph LANGE wrote:
> Hi Timothy,
>   thanks for your help.  I managed to convert the ontology.  But there were
> some problems, which you may take as bug reports for Protégé 4.1:
> 2010-01-08 12:36 Timothy Redmond <tredmond at>:
>> Otherwise you can set the java heap size to a large enough number [1] to
>> load the file.
> My first try was 1024M and that worked.  However, it was not sufficient to
> merely increase the heap size, but I also had to change a garbage collector
> setting (-XX:-UseGCOverheadLimit; see
I don't know a lot about this parameter.  I have seen the out of memory 
error that references this condition. But from the description it seems 
very likely that you should really set an even higher heap size.  
Spending 98% of the time doing fruitless garbage collection means that 
the application will perform very slowly.  In any case this is a jvm 
setting and except for documentation is out of the Protege groups control.
> Also, the output is first written to /tmp, which caused me another problem, as
> I have /tmp in a fixed-size RAM disk.  OK, this is pretty unusual, but still…
> You might consider documenting that behavior somewhere, and/or making
> Protégé's temp directory configurable.
It is not that unusual - traditionally /tmp can be smallish.  It turns 
out that this save to /tmp (protecting you from bad save operations) is 
done by the owl api.  I think that the easiest thing to do with this is 
to make it into a documentation bug.   It should be documented somewhere 
the allows you to change the temporary directory.

>> This does work fine in Protege 4.1 and the v3 version of the OWL API.
>> Neither of these are released yet but the OWL API v3 release is imminent
>> and hopefully the Protege 4.1 release will come very soon also.  If you
>> have java development tools there are instructions for building a copy
>> of Protege 4.1 here [2].
> 4.1 mostly worked, but I noticed two problems unrelated to my task:
> * FaCT++ is missing from the installation described on that wiki page, and it
>   was not available as a plugin in the respective user interface.
> * The ExplanationResultsView is broken (some class was not found).
Reasoners are a problem at the moment because things are in a bit of 
flux. The plan is that Protege 4.1 will be distributed with Hermit and 
FaCT++.  Pellet will be available for download.

Was the ExplanationResultsView exception a problem with startup?  Or did 
you enable it?

> Cheers,
> Christoph

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