Diabetes

Shaw et al., Reviewed NLP results for DM DBP. Seems that overall working well. Some descriptions of neuropathy are rarer than expected.

Crohn's and Ulcerative colitits

Ashwin et al., Discussed the AUC for UC and Crohn's with NLP and codified data. In this domain, once the cohort is roughly identified with the ICD-9 codes (low specificity), the NLP terms are much better than the codified terms in accurately identifying who has disease and who does not (as measured by AUC). Based on these analyses, it looks like PHS has 12000 (UC + Crohn's) of which about 3600 samples can be accumulated in one year.

Review NLP processes for our DBP's

Guergana et al,

Learning environment

1. Training/test set creation (labeling of data; currently using Knowtator (which itself used Protege 3.1))
2. Automated toolset (cTAKES + automated feature selection flow)
3. Loop 1-2

Inna Dubchak visit

Inna Dubchak from the LANL Joint Genome Institute gave an overview of her VISTA i2b2 docking project. This allows the VISTA i2b2 cell to provide analyses of the "meaning" of variants based largely on conservation data. Also gave an update on the rviewer tool

Technical Futures

Shawn, Kohane, NIch, Mike, Zak, Susanne, Bickel Discussed several important minimal commitment abstractions useful for temporal reasoning and for suggesting related queries.

Diabetes Mellitus + Autoimmune NLP definitions for cardiovascular disease

Shaw, Liao, Plenge et al., discussed our common needs on cardiovascular disease. The question of how detailed to go as opposed to a broad definition was reviewed. The tendency was to go in both directions.

Distributed queries

Griffin Weber, Shawn Murphy, Bill Simons, Susanne Churchill, Zak Kohane Discussed latest national developments for SHRINE queries. Very significant support and enthusiasm from the AUG. Reviewed temporal query capabilities and roadmap.