MDD

Perlis, Gainer, Churchill, Kohane, Weber

Anti-Depressant Pharmacogenetic Consortium led by Perlis with support from i2b2 is going to be launched soon.

NLP review by the psychiatrists on deck. It's hard slogging.

Early end to the day due to snow storm.

Core 2 and High Performance Computing

Valtchinov, Richter, Keogh, Weber, Kohane, Churchill

Reviewed high performance computing cell that is likely to be released in a few months.

Reviewed Relevance Network desk top application. Good progress but not yet ready for release.

Rheumatoid Arthritis

Wei, Plenge, Churchill, Kohane, Gainer, Murphy, Karlson, Tianxi, Szolovits, Churchill

Descriptive statistics of NLP corpus

30K (RA or CCP positive) -> Random 650 for chart review: 128 confirmed to have RA, 58 possible. This is gold standard review. So this means that there are radiologists (for example) coding RA where there is no RA, or rheumatologists coding for "rule out RA:

Tianxi reviewed feature selection via adaptive LASSO. Currently, the lower bound on the 95% confidence interval on the Positive Predictive Value seems to be high (stand by... we had an internal argument how the PPV was calculated)?

Major Depressive Disorder

Present: Iosifescu, Gainer, Churchill, Kohane, Zeng

Rate limiting step is now not the image processing of the MRI images, but the cycle from NLP identification of cases, submitted the case list to the MGH Radiology Department and then have the images stored on our scratch space server. Then the process of sorting through which images are complete enough, and then using Freesurfer to analyze them is relatively rapid.

Rheumatoid Arthritis

Plange, Karlson, Wei, Murphy, Kohane, Szolovits, Kohane, Gainer, Kat

Cases will be completed by January 1.

Controls to follow shortly thereafter.

i2b2 All Hands Meeting

Monthly i2b2 All Hand Meeting

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• Zak reviewed the internal i2b2 RFA's
• Peter Szolovits reviewed the results from the second annual NLP Challenge
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Scott Weiss introduced his vision of Personalized Medicine.

Included recent NEJM papers on SNP studies which showed modest contribution of SNP's over existing clinical indicators.

Normality

Present: Weber, Kohane, Gainer, Murphy

Discussed how to find control populations at length. Reviewed confounders and age-specific challenges. Discussed how various institution-specific and indepedent heuristics can be applied.

The i2b2 blog has moved

The prior version of this blog sits here. A very nice blog client I used on the Mac was no longer supported. So, I have had to migrate to this standard blogging environment with all the widely available tools. This blog is of very narrow interest. It documents some of the frequent meetings that drives i2b2, a National Center for Biomedical Computing.