Request for help:: NCBO Ontology Extraction Tool for i2b2

["Hari, Sekhar" <se...@cgi.com>]

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.