Before we go toward changes, lets just see if we need to. I would appreciate if each site could fill up attached form and send back to me. I filled some sites based on this discussion. Please, check and correct if I got it wrong. Alona.
On Wed, Jan 25, 2017 at 8:23 AM, Dan Connolly <dconno...@kumc.edu> wrote: > Changes in HERON ETL from result date to order date or specimen date would > take a month or two, depending on priorities. I suspect likewise at other > sites. > > If that sort of delay is acceptable, then I can proceed to get all 8 sites > to resolve this deference. > > On Jan 25, 2017 7:44 AM, Bernard Black <bbl...@kellogg.northwestern.edu> > wrote: > > Let me chime in, as project PI. > > This was a very helpful discussion. > > For this study, exact dates are not important. > > If blood was drawn on Tuesday, and results available on Friday, > > If as I suspect (but we can check) generally order date, specimen date, > and results date are all close, we can go with order date > > > > Bernie Black > > > > ************************************************************* > > Bernard S. Black > > Chabraja Professor, Northwestern University > > Pritzker Law School and Kellogg School of Management > > 375 East Chicago Ave., Chicago IL 60611 > > bbl...@northwestern.edu > > tel: law: 312-503-2784; Kellogg 847-491-5049; cell: 847-807-9599 > > papers on SSRN at: http://ssrn.com/author=16042 > > ************************************************************ > > > > *From:* Al'ona Furmanchuk [mailto:furmanc...@icnanotox.org] > *Sent:* Wednesday, January 25, 2017 7:31 AM > *To:* Campbell, James R <campb...@unmc.edu> > *Cc:* Phillip Reeder <phillip.ree...@utsouthwestern.edu>; < > gpc-dev@listserv.kumc.edu> <gpc-dev@listserv.kumc.edu>; Bernard Black < > bbl...@kellogg.northwestern.edu> > *Subject:* Re: [gpc-informatics] #551: next-D labs for cohort selection: > fasting glucose, HbA1c > > > > Guys, > > Order date is important for defining study sample and DM sample. specimen > date is important for "adherence to Treatment" variable. If difference in > dates is minor, we could uniformly switch to specimen date. But first we > have to know what is available in each site and ( if both dates are > available) how large is difference between dates? > > Sent from my iPhone > > > On Jan 24, 2017, at 10:40 PM, Campbell, James R <campb...@unmc.edu> wrote: > > I agree with Phillip. Clinically, the date/time reported for a lab test > is always when the patient had blood drawn or gave the sample. THAT is > when the patient was 'tested'. Nebraska records all lab test > observation_facts with START_DATE as date/time specimen was taken. We > record order time and result reported time separately. > > Jim > > James R. Campbell MD > > campb...@unmc.edu > > Office: 402-559-7505 <(402)%20559-7505> > > Secretary: 402-559-7299 <(402)%20559-7299> > > Pager: 402-888-1230 <(402)%20888-1230> > > > On Jan 24, 2017, at 6:07 PM, Al'ona Furmanchuk <furmanc...@icnanotox.org> > 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 <Phillip.Reeder@ > utsouthwestern.edu> 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 <gpc-dev-boun...@listserv.kumc.edu> on behalf of Dan > Connolly <dconno...@kumc.edu> > *Date: *Tuesday, January 24, 2017 at 5:09 PM > *To: *Al'ona Furmanchuk <furmanc...@icnanotox.org>, "< > gpc-dev@listserv.kumc.edu>" <gpc-dev@listserv.kumc.edu> > *Cc: *Bernard Black <bbl...@northwestern.edu> > *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=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=yqG12qsoyrBif-jILwubW8btm4qM0DM258CMGa2kQBI&s=B7cCQmEWUNYYqTWtUNzSvO_w9AgOsBJBy3wEyxt_Bms&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=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=yqG12qsoyrBif-jILwubW8btm4qM0DM258CMGa2kQBI&s=pGsz33DfC6KcCqKPa98qqkrDL6z3BB6KNoYcWjFZ0F0&e=> > > > -- > 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> 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=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=yqG12qsoyrBif-jILwubW8btm4qM0DM258CMGa2kQBI&s=pJR2npMPImLderrOyYqj8y314rhl5bxh_TdkjIazisA&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=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=yqG12qsoyrBif-jILwubW8btm4qM0DM258CMGa2kQBI&s=3Jny2FAhAcvq_hCSSoufzQEnkPPqO44JMAU_Zi_XbQs&e=> > > > > gpc-informatics <http://informatics.gpcnetwork.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=yqG12qsoyrBif-jILwubW8btm4qM0DM258CMGa2kQBI&s=b8Ln6oogSoCgdKEAkaGuJNxyO_HhjpaET5QTlwV-1gE&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=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=yqG12qsoyrBif-jILwubW8btm4qM0DM258CMGa2kQBI&s=VNFtxnmsnEgN7YNkkxnbm6_yI2aPx3BrxZLIEe8cUYc&e=> > E-mail: alona.furmanc...@northwestern.edu <furmanc...@icnanotox.org> > > 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=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=yqG12qsoyrBif-jILwubW8btm4qM0DM258CMGa2kQBI&s=VNFtxnmsnEgN7YNkkxnbm6_yI2aPx3BrxZLIEe8cUYc&e=> > E-mail: alona.furmanc...@northwestern.edu <furmanc...@icnanotox.org> > > Phone: 312-503-34281 > > _______________________________________________ > Gpc-dev mailing list > Gpc-dev@listserv.kumc.edu > http://listserv.kumc.edu/mailman/listinfo/gpc-dev > <https://urldefense.proofpoint.com/v2/url?u=http-3A__listserv.kumc.edu_mailman_listinfo_gpc-2Ddev&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE&m=yqG12qsoyrBif-jILwubW8btm4qM0DM258CMGa2kQBI&s=LiXNBizvgplZo4N_Bky-K6CsYVFaXT_dY3I6HIMrdCU&e=> > > > The information in this e-mail may be privileged and confidential, > intended only for the use of the addressee(s) above. Any unauthorized use > or disclosure of this information is prohibited. If you have received this > e-mail by mistake, please delete it and immediately contact the sender. > > > -- 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 <furmanc...@icnanotox.org> Phone: 312-503-34281
GPC-Capricorn-LabDates-2017-01-25-af.xlsx
Description: MS-Excel 2007 spreadsheet
_______________________________________________ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
