Gainer, Murphy, Shaw, Liao, Kohane, Churchill
Extensive discussion of which case cohort definition we will adopt for cardiovascular disease. Projected that discussion into the eventual endgame for molecular physiological characterization.
Specifics around EKG and echocardiogram reports reviewed.
Murphy, Weber, Churchill, McGow, Wilson, Kohane, Mendis
Reviewed community.i2b2.org. Specifically the i2b2 webclient as a first instance (this is a project that was first started by Griffin to work on top of the .NET stack) of bringing in a non-core project. Discussed how to prioritize tasks within a sponsored project.
We had an important but tangential discussion about the definition of episodes of care.
More than 20 participants. First, Kohane went over the outline of what i2b2 (v2) is going to focus on. Then reviewed recent AUG meeting and introduced Robert Plenge and Stanley Shaw who described the new DBP's of which they are PI.
We tagged the AUG meeting onto the national CTSA meeting. As you see from the pictures below, we had good attendance along with the 27 others attending via WEBEX.
Topics included
Brian Wilson presented the roadmap for i2b2(v2) for representation of genome-scale data ranging from SNP arrays to assembled full genomes or the short reads from which they were assembled. This preliminary roadmap is outlined below. Given the general interest of the GARLIC application domain (i.e. querying for patient populations with specified genome-scale characteristics) there are likely to be several national groups and/or users which have experience and interest. We plan to contact those we know of and appreciate other groups reaching out to help, collaborate or inform.
Ozlem, Guergana, Margarita, Jiaping Zeng, Pete Zak
Reviewed the co-reference NLP challenge and what needs to be done?
Discussed the challenges of combining packages with different open source licenses. The webservice API is generally seen as a useful way to keep packages with different licenses working together. The cost is the increased installation/dissemination complexity.
Ashwin (IBD) Ananthakrishnan, Philip L. De Jager (MS), Beth Karlson, Helena Canhão, Kat, Sordo, Guergana, Stan, Peter Szolovits, Robert Plenge, Raoul Guzman, Vivian Gainer, Xia Zongqi (Neuro-rheumatology), LJ Wei, Peter Szolovits, Tianxi Cai
The PI's described how they propose to build on the experience of the RA DBP to go into further depth into the phenotypes (around RA) and drug effects/efficacy and see how far we can go with EHR-derived phenotypes. Further, we will be studying the shared and differing pathotypes across a larger range of autoimmune diseases, namely including inflammatory bowel disease and multiple sclerosis (for which we have expert representation in this DBP). We also reviewed the imperative to identify subcohorts (based on combinations of clinical and genomic stratification) that have distinguishing therapeutic efficacy and/or adverse events.
Present: Susanne Churchill, Ozlem, Zak, Guergana, Griffin Weber, Dan Nigrin
Welcome to my first blog post in the recompeted i2b2.
We discussed temporal reasoning requirements in the new i2b2. Requirements for interval and point logic and how we were informed by Nigrin's master thesis reviewed. Integration of NLP derived temporal relations was preliminarily reviewed.
Present: Stan Shaw, Vivian Gainer, Margarita Sordo. Kat, Susanne Churchill, Ozlem, Zak, Guergana
The new DBP led by Stan Shaw addresses the epigenetics (DNA methylation, histone acetylation, histone methylation assayed using full genome-scale resequencing) of heart disease in the context of diabetes mellitus.
Kat reviewed the overall approach that we take in DBP's in defining cohorts through billing code,
Ozlem gave an update on the new de-identification pipeline.
We reviewed which fellow we might find to do some of the heavy lifting with Stan.
