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.