The patient demographics are stored in our i2b2 in the person dimension. The QA scripts are written with the assumption that all data is stored in the fact table. There is no provision for the script to leverage the ontology architecture to determine the storage location of the various pieces of data. I'm sure it was done that way to simplify the script, but it does ignore a pretty major feature of i2b2: the ontology mapping functionality. This makes it less portable to sites that have a different implementation of the ontology. I don't characterize a difference in implementation a problem in the data warehouse.
Keep in mind that MU had an i2b2 instance back in 2014, and the MU architecture was established before joining the GPC. It would be work to either shift our demographics storage (and additional storage capacity), or to rewrite the QA scripts. We will opt to rewrite the QA scripts, but to do it in a portable way (i.e. we could share our changes back to the GPC) will require some complexity of coding to leverage the ontology framework in i2b2. We may have to opt for hardcoding our version against the dimension table. Aside from that, we still have the relatively simple task of mapping our concept codes/paths to get the remainder (non-demographic part) of the script to work correctly. Tim From: Mosa, Abu S. Sent: Monday, February 15, 2016 10:20 AM To: Dan Connolly Cc: <[email protected]>; Green, Timothy A.; McNeeley, Todd A. Subject: RE: Gather 2015 4th quarterly QA results I would defer this to Tim and Todd to share their thoughts on this. Thanks. --Mosa From: Dan Connolly [mailto:[email protected]] Sent: Monday, February 15, 2016 10:03 AM To: Mosa, Abu S. <[email protected]<mailto:[email protected]>> Cc: <[email protected]<mailto:[email protected]>> <[email protected]<mailto:[email protected]>> Subject: RE: Gather 2015 4th quarterly QA results What are the symptoms when you try to run the QA scripts, Mosa? What diagnostics do you get? The premise of the QA scripts is that if they don't run, that's a problem with your data warehouse. Perhaps there are actually problems with the scripts, but if so, we need details on what those problems are. Also, we have a shared source code repository in gpc-qa-quarterly<https://bitbucket.org/gpcnetwork/gpc-qa-quarterly>. So if you make changes, please strive to make them portable to other sites. p.s. I presume it's OK to share this thread with gpc-dev, as it regards group technical work. -- Dan ________________________________ From: Mosa, Abu S. [[email protected]] Sent: Friday, February 12, 2016 4:41 PM To: Dan Connolly Subject: Gather 2015 4th quarterly QA results Hi Dan, I talked with our technical team about generating the 2015 4th quarterly report. They looked into the MSSQL code that you referred to me on BitBucket. They advised that major re-writing effort is needed in order to localize the scripts to be able to run on our i2b2 data model. They are currently focusing on the Phase I implementation (specifically tumor registry data load) which they target to complete by end of this month. So, a viable timeline for generating the 2015 4th quarterly report for us would be Mid-march. Let me know if you have any questions. If needed, we can discuss this during the next Dev call. Regards, Abu Saleh Mohammad Mosa, PhD Director, Research Informatics Institute for Clinical and Translational Science University of Missouri
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