*Dan:* It is important to be clear what each site use under "start_date". Especially for cases when ORDER_DATE is different from SPECIMEN_TAKEN_DATE. I appreciate, Dan if you could gather this info. It is important to be on the same terms when collecting data to the table 1. *Phillip:* I agree that having order, specimen and result dates is good practice. This is what we have here at NU as well.
Alona. On Tue, Jan 24, 2017 at 5:49 PM, Phillip Reeder < [email protected]> wrote: > I’d recommend using the SPECIMEN_TAKEN_DATE/TIME for the start_date of a > lab. I believe it is the more clinically correct time as the results of > labs can sometimes take days to return. We use the specimen time, followed > by the result time, I believe. > > For the PCORI CDM, I plan on putting all of the needed date/times, > (specimen, order, and result) into a small XML block in the > observation_blob column so that I can have all the times when I ETL the > data to the CDM schema. > > Phillip > > From: Gpc-dev <[email protected]> on behalf of Dan > Connolly <[email protected]> > Date: Tuesday, January 24, 2017 at 5:09 PM > To: Al'ona Furmanchuk <[email protected]>, "< > [email protected]>" <[email protected]> > Cc: Bernard Black <[email protected]> > Subject: RE: [gpc-informatics] #551: next-D labs for cohort selection: > fasting glucose, HbA1c > > 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 [[email protected]] > *Sent:* Tuesday, January 24, 2017 4:35 PM > *To:* <[email protected]> > *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 <[email protected]> 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: [email protected] <[email protected]> > Phone: 312-503-34281 > > ------------------------------ > > UT Southwestern > > Medical Center > > The future of medicine, today. > -- 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: [email protected] <[email protected]> Phone: 312-503-34281
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