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<mailto:campb...@unmc.edu>
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230

On Jan 24, 2017, at 6:07 PM, Al'ona Furmanchuk 
<furmanc...@icnanotox.org<mailto: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.ree...@utsouthwestern.edu<mailto:phillip.ree...@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<mailto:gpc-dev-boun...@listserv.kumc.edu>> 
on behalf of Dan Connolly <dconno...@kumc.edu<mailto:dconno...@kumc.edu>>
Date: Tuesday, January 24, 2017 at 5:09 PM
To: Al'ona Furmanchuk 
<furmanc...@icnanotox.org<mailto:furmanc...@icnanotox.org>>, 
"<gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>>" 
<gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>>
Cc: Bernard Black <bbl...@northwestern.edu<mailto: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://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<mailto:furmanc...@icnanotox.org>]
Sent: Tuesday, January 24, 2017 4:35 PM
To: <gpc-dev@listserv.kumc.edu<mailto: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

________________________________

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: alona.furmanc...@northwestern.edu<mailto:furmanc...@icnanotox.org>
Phone: 312-503-34281
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