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From Pei Chen <chen...@apache.org>
Subject Re: Request for help:: NCBO Ontology Extraction Tool for i2b2
Date Thu, 23 Apr 2015 15:52:23 GMT
Is it happening to all of the ontologies you mentioned or just one?  Those
ontologies do not seem very big or deep.  Did you notice in the logs if
something in the ontology having some sort of circular reference or causing
an infinite loop?
I think lori from i2b2 may be better at answering this since this isn't
exactly cTAKES related...

On Wed, Apr 22, 2015 at 7:21 AM, Hari, Sekhar <sekhar.hari@cgi.com> wrote:

> Hello there -
> Introducing myself:
> My name is Sekhar Hari, responsible for Bio-informatics products/
> solutions in CGI, a Canadian company. In this capacity, I am also
> responsible for developing a software to identify potential adverse events
> and serious adverse events in healthcare settings.
> I have been trying to extract and process few Ontologies using the latest
> version of NCBO Ontology Extraction Tool to load into I2B2 but with no
> luck. I could extract the staging file, and can load this into the  I2B2
> staging table. However, when I run the
> edu.harvard.i2b2.ncbo.extraction.NCBOOntologyProcessAll program, it always
> fails with GCOverheadLimit. I tried by increasing the JVM memory to 8GB but
> no result. My hardware resource is limited at present, and I can't increase
> the JVM memory size beyond 8GB.
> As I have a demo for a large hospital coming up soon, in the interest of
> time, would you be kind enough to extract and process the following
> ontologies, and upload the final metadata file here?
> http://i2b2.bioontology.org/
> Ontology IDs:
> 1.       WHO-ART
> 2.       OAE
> 3.       SSE
> 4.       OVAE
> The user-guide that I was following is attached.
> Many thanks in advance.
> Regards,
> Sekhar H.

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