(Please excuse the awkward top-posting format; I'm stuck with Microsoft Outlook.)
Perhaps we're converging... the new Data Builder code<https://informatics.gpcnetwork.org/trac/Project/ticket/134#comment:4> delivers an sqlite3 file, so you can continue to use SQL to analyze it; and if you like python or Java better than R for post-SQL work, that's fine too. But note that each Data Builder result is based on an i2b2 patient set that came from and audited i2b2 query. We don't have governance to let investigators run arbitrary SQL queries on our whole clinical data warehouse and we don't plan to (neither KUMC HERON nor GPC). For the 3 initial cohorts, we can get away with ad-hoc one-off work, but for GPC work in general, we plan do use i2b2 to do as much of the querying as we can. -- Dan ________________________________ From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on behalf of Alex Bokov [bo...@uthscsa.edu] Sent: Monday, October 06, 2014 5:05 PM To: gpc-dev@listserv.kumc.edu Subject: Re: Example (Re: Empirical Data Dictionary) [...] I've seen pretty good cohort characterization progress w.r.t. breast cancer and ALS based on HERON data builder results (which are analagous to i2b2 PDO results as seen in the timeline plug-in). I don't understand why that approach isn't suitable. I haven't had a chance to look at the ALS script they posted yet, I need to do that, I may learn some useful stuff. Are you saying there is now a way to get PDOs or data builder results into a denormalized tabular format that can be analyzed in SAS or R? Because that was the main problem I encountered before meeting with success just using SQL. I decided that I'd fall back on R only after I hit a problem SQL couldn't handle, and so far this hasn't happened. Also, much as I like R, there is a lot more SQL expertise in the GPC than R expertise, and everyone already has some type of SQL database because I2B2 requires it. So a suitably dialect-independent SQL script is easier to deploy than convincing everyone to add R to their toolchain.
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