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.
