Reviewing the HERON ETL code, I see it does populate the i2b2 start_date for labs from Epic's result_time, which looks more like RESULT_DATE.
I see that our code to build the PCORNet LAB_RESULT_CM.LAB_ORDER_DATE (PCORNetLoader_ora.sql#L1407<https://github.com/kumc-bmi/i2p-transform/blob/cycle_2/Oracle/PCORNetLoader_ora.sql#L1407>) uses this start_date that came from result_time, so we're fudging things a bit there. The HERON ETL code is used at KUMC and was the basis of work at UTHSCSA and UNMC. If the difference between LAB_ORDER_DATE and RESULT_DATE is significant for Next-D, I can find out how the other participating GPC sites do start_date for labs. ref: * heron_load/epic_labs_transform.sql<https://informatics.kumc.edu/work/browser/heron_load/epic_labs_transform.sql> -- Dan ________________________________ From: Al'ona Furmanchuk [furmanc...@icnanotox.org] Sent: Tuesday, January 24, 2017 4:35 PM To: <gpc-dev@listserv.kumc.edu> Cc: Mei Liu; Dan Connolly; Taylor, Bradley; Bernard Black Subject: Re: [gpc-informatics] #551: next-D labs for cohort selection: fasting glucose, HbA1c Dan, great job! Meanwhile, could you please clarify actual meaning of "start_date" in i2b2? Is it more like "LAB_OERDER_DATE" (when lab was ordered), "SPECIMEN_DATE" (when specimen was taken), "RESULT_DATE" (when results became available)? Alona. On Tue, Jan 24, 2017 at 4:06 PM, GPC Informatics <d...@madmode.com<mailto:d...@madmode.com>> wrote: #551: next-D labs for cohort selection: fasting glucose, HbA1c --------------------------+----------------------- Reporter: afurmanchuk | Owner: meiliu Type: design-issue | Status: accepted Priority: major | Milestone: next-d Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: 545 | --------------------------+----------------------- Comment (by dconnolly): Alona, Mei, I managed to prototype using i2b2 and LOINC codes: - 8f27bee get FG_Intial, RG_Initial from i2b2 star schema \\[https://github.com/dckc/nextd-study- support/blob/master/NextDvariableExtractionOracleTable1GPC.sql#L138-L221 NextDvariableExtractionOracleTable1GPC.sql lines 138-221] At KUMC, this results in ~500K rows in RG_Intial but 0 in FG_Intial: as I noted in comment:1, the LOINC code KU Hospital maps to (`Glucose SerPl-mCnc (2345-7)`) doesn't distinguish fasting from eating. Some changes were perhaps substantive, so I need you to evaluate the impact: - LAB_ORDER_DATE became start_date, which is more likely result date than order date - i2b2 start_date includes time Brad, I think this approach should work at other GPC sites. I'd appreciate if you'd (have George) take a look. -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/551#comment:8> gpc-informatics <http://informatics.gpcnetwork.org/> Greater Plains Network - Informatics -- Al’ona Furmanchuk, Ph.D. Research Associate Center for Health Information Partnerships, Northwestern University, Feinberg School of Medicine 633 N. Saint Clair Street, 20th floor, Chicago, IL 60611 Web: http://furmanchuk.com/ E-mail: alona.furmanc...@northwestern.edu<mailto:furmanc...@icnanotox.org> Phone: 312-503-34281
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