Diabetes and CVD

Stan shaw led a discussion of inflammatory markers in the diabetes population.

i2b2 EAC

March 24th, External Advisory Committee came to Boston for a visit.

The EAC is constituted of:

Daniel Masys (chair), Vanderbilt University

Elmer Bernstam, University of Texas at Houston

Lisa Cannon-Albright, University of Utah

Peter Tarczy-Hornoch, University of Washington, Seattle

George Hripczak, Columbia University

NIH representative: Valerie Florance, NLM project officer

Very productive meeting with useful directional advice from the EAC.

i2b2 All Hands Meeting

Eric Perakslis PhD presented his work on i2b2 in the J&J context and beyond with tranSMART. Interestingly, this i2b2 instance is hosted on the Amazon EC2 cloud. He had the temerity to run a live demo which worked flawlessly. Good Karma! Also the involvement of tranSMART with the Innovative Medicines Initiative in Europe with significant uptake by pharmaceutical industry (i.e. GSK/ECLIPSE, AstraZeneca, Pfizer, Novartis) was intriguing and encouraging.

His slide show is available here.

Other i2b2 business reviewed including the very success i2b2/NCBO tutorial last week at AMIA in San Francisco and the other SHRINE implementations that are occurring nationally.

Epigenetics

Shaw, Kohane, Kasif, Plenge, Churchill, Liao, Murphy, Savova

Extensive discussions about which epigenetics marks are best captured from clinical discards and under what hypotheses.

Autoimmune DBP

Savova reported that the new cTAKES pipeline is up and running against the production system.

Plenge reported on the state on the new RA datamart.

Liao has finished the chart reviews of a random sample of the 4500 RA patients. 10% had coronary artery disease. Of that 10%, 41% have definite CAD and 27% have probable CAD.

Feena provided an update on the sequencing project: 500 cases and 650 controls. Discussed a lot of the travails of de-"noising" and de-"batching" the variation found in the pooled samples (done without barcoding).

i2b2 Mapping Cell

Review of the annotation procedures for NLP (in context of RA-CVD and multiple sclerosis).

Present: Murphy, Savova, Szolovits, Liao, Cai, Xia, Gainer, Raoul, Kohane, Churchill

In a discussion led by Guergana Savova, we reviewed the Knowtator package that is built on top of PROTÉGÉ. The focus of the discussion was on the "squishy" and detailed assessments of patient functioning (e.g. "bending", "grasping", "doing housework" etc). We also discussed comparing the "bag of words" classification approach vs. the fine-grained sentence-level or concept-level annotation.