Phillip, I've started hacking on the SCILHS->CDM code<https://informatics.gpcnetwork.org/trac/Project/ticket/476#comment:6> (I forked the SCILHS repositories on github/njgraham<https://github.com/njgraham>). I think I'm seeing the same race vs. ethnicity issue you logged (Ethnicity issue #1<https://github.com/SCILHS/i2p-transform/issues/1>). See comment in PCORNetLoader_ora.sql, around line 800<https://github.com/njgraham/i2p-transform/blob/master/Oracle/PCORNetLoader_ora.sql#L800>.
Anyway, most of my changes thus far have been stubs, etc. to just get the code running but I've tried to add TODOs/comments as I go. I suspect some of the TODOs may turn in to issues I log and others I'll remove as I figure out what's going on. Have you ended up making more changes than you noted in the thread below? Do you have your changes shared somewhere? Thanks! Regards, Nathan From: gpc-dev-boun...@listserv.kumc.edu [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly Sent: Monday, February 15, 2016 12:37 PM To: Phillip Reeder; gpc-dev@listserv.kumc.edu Subject: IN / LIKE limitation RE: SCILHS i2b2 to CDM on Oracle Re IN / LIKE #2, would you please open an i2p-transform issue<https://github.com/SCILHS/i2p-transform/issues>? -- Dan ________________________________ From: gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu> [gpc-dev-boun...@listserv.kumc.edu] on behalf of Phillip Reeder [phillip.ree...@utsouthwestern.edu] Sent: Wednesday, February 10, 2016 12:12 PM To: gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu> Subject: SCILHS i2b2 to CDM on Oracle Has anyone else attempted the SCILHS i2b2 to CDM code on Oracle? I'm focusing on the demographics table to start with have run into a few things I wanted to share. #1) SCILHS relies on the patient_dimension for the demographics, not the observation_fact. Just something to be aware of, not really a problem as long as you have the patient_dimension built out. #2) The demographics ontology has some rows that use the IN for the operator and some rows that use like. But the code only works for the race/sex where it is using "IN" as the operator. I added a where race.c_operator='IN' , sex.c_operator='IN' , hisp.c_operator='IN' where necessary to avoid the oracle error. #3) For Hispanic, the code is only looking at the race_cd. This only give you 'Yes' or 'No-Information' as values. I think it would make more sense to move the ethnicity information to an ethnicity_cd column. Anyone else working with the i2b2 to CDM on Oracle code? Just wondering if there are any other changes you've had to make to get it working. Thanks, Phillip ________________________________ UT Southwestern Medical Center The future of medicine, today.
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