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

Christoph LANGE ch.lange at
Tue Jan 12 15:09:58 PST 2010

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

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.

> 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).



Christoph Lange, Jacobs Univ. Bremen,, Skype duke4701
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