Dan and others: It seems useful to know which “date” each site uses. And the resulting paper(s) will read cleaner if we can obtain the same date from all or most of the GPC sites. Other than that, I doubt it will matter much which date we used. I can see advantages to the order date, and different advantages to the results date. But the differences are not large enough to justify keeping multiple dates. This is why I suggested using “order date” But if only some sites have order date, and all have “specimen date” or all have “results date”, we’ll be better off using a date that is common across sites. So we should find out – and Alona is trying to determine this – which sites use which dates.
Bernie ************************************************************* Bernard S. Black Chabraja Professor, Northwestern University Pritzker Law School and Kellogg School of Management 375 East Chicago Ave., Chicago IL 60611 [email protected]<mailto:[email protected]> tel: law: 312-503-2784<tel:312-503-2784>; Kellogg 847-491-5049<tel:847-491-5049>; cell: 847-807-9599<tel:847-807-9599> papers on SSRN at: http://ssrn.com/author=16042 ************************************************************ From: Dan Connolly [mailto:[email protected]] Sent: Wednesday, January 25, 2017 8:15 AM To: Al'ona Furmanchuk <[email protected]> Cc: Bernard Black <[email protected]>; <[email protected]> <[email protected]>; Phillip Reeder <[email protected]> Subject: Re: [gpc-informatics] #551: next-D labs for cohort selection: fasting glucose, HbA1c Why is the difference important? How does it affect the initial next-d cohort calculations? On Jan 24, 2017 6:06 PM, Al'ona Furmanchuk <[email protected]<mailto:[email protected]>> wrote: 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]<mailto:[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]<mailto:[email protected]>> on behalf of Dan Connolly <[email protected]<mailto:[email protected]>> Date: Tuesday, January 24, 2017 at 5:09 PM To: Al'ona Furmanchuk <[email protected]<mailto:[email protected]>>, "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[email protected]>> Cc: Bernard Black <[email protected]<mailto:[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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_kumc-2Dbmi_i2p-2Dtransform_blob_cycle-5F2_Oracle_PCORNetLoader-5Fora.sql-23L1407&d=CwMGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=r-3hWL7GRVhUhyXY6FfVUluKJR3bYbrGXcwJilMRsew&s=15mzJs5mBXRjJaVBF517lyXrKZpf8T34ormHaKg3LFc&e=>) 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://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.kumc.edu_work_browser_heron-5Fload_epic-5Flabs-5Ftransform.sql&d=CwMGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=r-3hWL7GRVhUhyXY6FfVUluKJR3bYbrGXcwJilMRsew&s=hPyeoTk1rxBs-KcUqIi63F2281dWVsMxm6MfqeIfCBQ&e=> -- Dan ________________________________ From: Al'ona Furmanchuk [[email protected]<mailto:[email protected]>] Sent: Tuesday, January 24, 2017 4:35 PM To: <[email protected]<mailto:[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]<mailto:[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-<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dckc_nextd-2Dstudy-2D&d=CwMGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=r-3hWL7GRVhUhyXY6FfVUluKJR3bYbrGXcwJilMRsew&s=8cIZsVCmoyoDjBW1tGTb_prwDMN_IGgft8UXuxzU_ow&e=> 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_trac_Project_ticket_551-23comment-3A8&d=CwMGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=r-3hWL7GRVhUhyXY6FfVUluKJR3bYbrGXcwJilMRsew&s=q5XRCs9mpObkPc7ulpQzfsw9Jn3rFVbETfMjt3trCXs&e=>> gpc-informatics <http://informatics.gpcnetwork.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_&d=CwMGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=r-3hWL7GRVhUhyXY6FfVUluKJR3bYbrGXcwJilMRsew&s=ogeoxsPD0aMC7FuqpUSmDhs8rZZLMqOIUDFV8EHTGVw&e=>> 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/<https://urldefense.proofpoint.com/v2/url?u=http-3A__furmanchuk.com_&d=CwMGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=r-3hWL7GRVhUhyXY6FfVUluKJR3bYbrGXcwJilMRsew&s=GJaQ7Yh0_yh-o6TOQemgACkph54eT5Alffcxd-ZHmpU&e=> E-mail: [email protected]<mailto:[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/<https://urldefense.proofpoint.com/v2/url?u=http-3A__furmanchuk.com_&d=CwMGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=r-3hWL7GRVhUhyXY6FfVUluKJR3bYbrGXcwJilMRsew&s=GJaQ7Yh0_yh-o6TOQemgACkph54eT5Alffcxd-ZHmpU&e=> E-mail: [email protected]<mailto:[email protected]> Phone: 312-503-34281
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