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.

Inflammatory Bowel Disease

Ashwin presented

Reviewed the NLP approach to date.

Showed the distinctions made based on terms of varying specificity. The NLP processing increased the accuracy as expected but probably by only 10% relative to the codified data. However the codified data alone had much less stable performance, probably because those are easier to overfit to local billing practice and demographics of the underlying hospital population.

Also reviewed when to start sample collection.

i2b2 Version 1.6 release preparations

Kohane, Churchill, Murphy, Mendis, Wattansin Last minute preparation for documentation and squishing any remaining bugs.

DM/CVD

Stan Shaw, Tianxi Cai, Raoul, Shawn, Zak, Susanne et al.,

Discussed whether to expand the data mart to include other hospitals.

Reviewed study design for measures of inflammation.