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From "Hari, Sekhar" <sekhar.h...@cgi.com>
Subject Request for help:: NCBO Ontology Extraction Tool for i2b2
Date Wed, 22 Apr 2015 11:21:43 GMT
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.

Sekhar H.

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