date:20170901

Re: PCORI CDM Lab Issue

2017-09-01 Thread Campbell, James R

The 11000+common labs we are setting up for our SNOW-SHRINE node are planned to 
have common lab names derived from LOINC and we also plan to put together our 
result ranges into metadataxml that can support result checking and query by 
value.  We presume that those with quantitative results can have metadataxml 
easily converted to LAB_RESULT_CM result ranges.  We would love to share the 
work on the metadataxml development if others in GPC have already done any work.
Jim

James R. Campbell MD
campb...@unmc.edu
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230

On Aug 31, 2017, at 6:08 PM, Phillip Reeder 
mailto:phillip.ree...@utsouthwestern.edu>> 
wrote:

CAUTION: This email is not from a UNMC or Nebraska Medicine source. Only click 
links or open attachments you know are safe.
Our CDM report showed us failing the check 3.10 for "LAB_NAME is a common 
measure* or LAB_LOINC is not null and RESULT_NUM is not null and 
NORM_MODIFIER_LOW, NORM_RANGE_LOW, NORM_MODIFIER_HIGH, and NORM_RANGE_HIGH are 
all populated per CDM specifications.**”

The difference between 3.09 and 3.10 seems to be the normal ranges, but we do 
have normal ranges in our data as we used the i2p code to generate the lab 
results.  Did anyone else have an issue like this with their last EDC report?  
Does anyone understand the SAS code well enough to help me figure out why this 
check was failing for us?

Thanks,
Phillip



UT Southwestern


Medical Center



The future of medicine, today.


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RE: Running CDM queries for CTSA program to calculate Common Metrics.

2017-09-01 Thread Rosemond, Erica (NIH/NCATS) [E]

Excellent!  Thank you!

Erica

From: McClay, James C [mailto:jmcc...@unmc.edu]
Sent: Friday, September 1, 2017 2:21 PM
To: Russ Waitman ; GPC-DEV@LISTSERV.KUMC.EDU
Cc: Rosemond, Erica (NIH/NCATS) [E] ; 
'clar...@uthscsa.edu' (clar...@uthscsa.edu) 
Subject: RE: Running CDM queries for CTSA program to calculate Common Metrics.

Hi Russ, Erica,
We're not a CTSA site but I ran the query without trouble (3m 51s)

James McClay, MD, MS, FACEP
Associate Professor, Emergency Medicine
Chair, UNMC Biomedical Informatics Program
981150 Nebraska Medical Center
Omaha, NE 68198-1150
jmcc...@unmc.edu
www.linkedin.com/in/infodoc
Twitter: @jmcclay
402-559-3587

From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Russ 
Waitman
Sent: Friday, September 01, 2017 12:37 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Cc: 'rosemo...@mail.nih.gov' 
mailto:rosemo...@mail.nih.gov>>; 'clar...@uthscsa.edu' 
(clar...@uthscsa.edu) 
mailto:clar...@uthscsa.edu>>
Subject: Running CDM queries for CTSA program to calculate Common Metrics.

CAUTION: This email is not from a UNMC or Nebraska Medicine source. Only click 
links or open attachments you know are safe.
Hi Everyone,

You may already know this but I am on the CTSA call with the other sites and 
Erica Rosemond at NIH has worked with the San Antonio team to develop CTSA 
Informatics Common Metrics against the PCORnet CDM (kudos UTHSC-SA!) and also 
OMOP.

They are looking for people to pilot the scripts
https://github.com/ncats/CTSA-Metrics

Let Dr. Rosemond (cced) know if you want to pilot.

Erica: Maren Wennberg on our team at KUMC can run those for you.  Maren: can 
you check the scripts wrt if I should log it with the DROC as a feasibility or 
a DUA.  I think it's just Counts and I don't need to do a DUA.

Russ Waitman, PhD
Director of Medical Informatics
Associate Vice Chancellor for Enterprise Analytics
Professor, Department of Internal Medicine
University of Kansas Medical Center, Kansas City, Kansas
913-945-7087 (office)
rwait...@kumc.edu
http://www.kumc.edu/ea-mi/
http://informatics.kumc.edu
http://www.gpcnetwork.org - a PCORnet collaborative 
www.pcornet.org

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.
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Re: Running CDM queries for CTSA program to calculate Common Metrics.

2017-09-01 Thread Kristi Holmes

Terrific news…and this Nebraska native is delighted to see input from the UNMC 
team!
Thank you again for the input,
Kristi


Kristi L. Holmes, PhD
Director, Galter Health Sciences Library
Associate Professor, Preventive Medicine (Health and Biomedical Informatics)
Director of Evaluation, Northwestern University Clinical and Translational 
Sciences Institute

Northwestern University Feinberg School of Medicine
303 East Chicago Avenue, Suite 2-213
Chicago, Illinois 60611
312.503.8133 office
kristi.hol...@northwestern.edu
galter.northwestern.edu

Assistant: Rebecca Corona 
r-cor...@northwestern.edu

[cid:image001.png@01D32327.81040F60]



From: Erica Rosemond 
Date: Friday, September 1, 2017 at 1:28 PM
To: "McClay, James C" , Russ Waitman , 
"GPC-DEV@LISTSERV.KUMC.EDU" 
Cc: "'clar...@uthscsa.edu' (clar...@uthscsa.edu)" , Justin 
B Starren , Kenneth Gersing 
, Kristi Holmes 
Subject: RE: Running CDM queries for CTSA program to calculate Common Metrics.

Excellent!  Thank you!

Erica

From: McClay, James C [mailto:jmcc...@unmc.edu]
Sent: Friday, September 1, 2017 2:21 PM
To: Russ Waitman ; GPC-DEV@LISTSERV.KUMC.EDU
Cc: Rosemond, Erica (NIH/NCATS) [E] ; 
'clar...@uthscsa.edu' (clar...@uthscsa.edu) 
Subject: RE: Running CDM queries for CTSA program to calculate Common Metrics.

Hi Russ, Erica,
We’re not a CTSA site but I ran the query without trouble (3m 51s)



James McClay, MD, MS, FACEP
Associate Professor, Emergency Medicine
Chair, UNMC Biomedical Informatics Program
981150 Nebraska Medical Center
Omaha, NE 68198-1150
jmcc...@unmc.edu
www.linkedin.com/in/infodoc
Twitter: @jmcclay
402-559-3587

From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Russ 
Waitman
Sent: Friday, September 01, 2017 12:37 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Cc: 'rosemo...@mail.nih.gov' 
mailto:rosemo...@mail.nih.gov>>; 'clar...@uthscsa.edu' 
(clar...@uthscsa.edu) 
mailto:clar...@uthscsa.edu>>
Subject: Running CDM queries for CTSA program to calculate Common Metrics.

CAUTION: This email is not from a UNMC or Nebraska Medicine source. Only click 
links or open attachments you know are safe.
Hi Everyone,

You may already know this but I am on the CTSA call with the other sites and 
Erica Rosemond at NIH has worked with the San Antonio team to develop CTSA 
Informatics Common Metrics against the PCORnet CDM (kudos UTHSC-SA!) and also 
OMOP.

They are looking for people to pilot the scripts
https://github.com/ncats/CTSA-Metrics

Let Dr. Rosemond (cced) know if you want to pilot.

Erica: Maren Wennberg on our team at KUMC can run those for you.  Maren: can 
you check the scripts wrt if I should log it with the DROC as a feasibility or 
a DUA.  I think it’s just Counts and I don’t need to do a DUA.

Russ Waitman, PhD
Director of Medical Informatics
Associate Vice Chancellor for Enterprise Analytics
Professor, Department of Internal Medicine
University of Kansas Medical Center, Kansas City, Kansas
913-945-7087 (office)
rwait...@kumc.edu
http://www.kumc.edu/ea-mi/
http://informatics.kumc.edu
http://www.gpcnetwork.org
 – a PCORnet collaborative 
www.pcornet.org


The information in this e-mail may be privilege

RE: Running CDM queries for CTSA program to calculate Common Metrics.

2017-09-01 Thread McClay, James C

Hi Russ, Erica,
We're not a CTSA site but I ran the query without trouble (3m 51s)



James McClay, MD, MS, FACEP
Associate Professor, Emergency Medicine
Chair, UNMC Biomedical Informatics Program
981150 Nebraska Medical Center
Omaha, NE 68198-1150
jmcc...@unmc.edu
www.linkedin.com/in/infodoc
Twitter: @jmcclay
402-559-3587

From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Russ 
Waitman
Sent: Friday, September 01, 2017 12:37 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Cc: 'rosemo...@mail.nih.gov' ; 'clar...@uthscsa.edu' 
(clar...@uthscsa.edu) 
Subject: Running CDM queries for CTSA program to calculate Common Metrics.

CAUTION: This email is not from a UNMC or Nebraska Medicine source. Only click 
links or open attachments you know are safe.

Hi Everyone,

You may already know this but I am on the CTSA call with the other sites and 
Erica Rosemond at NIH has worked with the San Antonio team to develop CTSA 
Informatics Common Metrics against the PCORnet CDM (kudos UTHSC-SA!) and also 
OMOP.

They are looking for people to pilot the scripts
https://github.com/ncats/CTSA-Metrics

Let Dr. Rosemond (cced) know if you want to pilot.

Erica: Maren Wennberg on our team at KUMC can run those for you.  Maren: can 
you check the scripts wrt if I should log it with the DROC as a feasibility or 
a DUA.  I think it's just Counts and I don't need to do a DUA.

Russ Waitman, PhD
Director of Medical Informatics
Associate Vice Chancellor for Enterprise Analytics
Professor, Department of Internal Medicine
University of Kansas Medical Center, Kansas City, Kansas
913-945-7087 (office)
rwait...@kumc.edu
http://www.kumc.edu/ea-mi/
http://informatics.kumc.edu
http://www.gpcnetwork.org - a PCORnet collaborative 
www.pcornet.org


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.
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RE: Running CDM queries for CTSA program to calculate Common Metrics.

2017-09-01 Thread Rosemond, Erica (NIH/NCATS) [E]

Hi Brad,

Thank you!!  If you have questions for the development team I am cc-ing them 
(Justin Starren, Kristi Holmes, Ken Gersing, me).

Best,
Erica

-Original Message-
From: Taylor, Bradley [mailto:btay...@mcw.edu] 
Sent: Friday, September 1, 2017 1:45 PM
To: Russ Waitman ; GPC-DEV@LISTSERV.KUMC.EDU
Cc: Rosemond, Erica (NIH/NCATS) [E] ; 
'clar...@uthscsa.edu' (clar...@uthscsa.edu) 
Subject: Re: Running CDM queries for CTSA program to calculate Common Metrics.

It’s just counts. I just ran it against our CDM and got results back. I do have 
a couple of questions though.

Regards,
Brad

Bradley W. Taylor
Chief Research Informatics Officer
Medical College of Wisconsin
Co-Director Biomedical Informatics
Clinical and Translational Science Institute Site-PI PCORNet Greater Plains 
(GPC) CDRN
e: btay...@mcw.edu
p: 414-805-7307


From: Gpc-dev  on behalf of Russ Waitman 

Date: Friday, September 1, 2017 at 12:37 PM
To: "GPC-DEV@LISTSERV.KUMC.EDU" 
Cc: "'rosemo...@mail.nih.gov'" , "'clar...@uthscsa.edu' 
(clar...@uthscsa.edu)" 
Subject: Running CDM queries for CTSA program to calculate Common Metrics.

Hi Everyone,

You may already know this but I am on the CTSA call with the other sites and 
Erica Rosemond at NIH has worked with the San Antonio team to develop CTSA 
Informatics Common Metrics against the PCORnet CDM (kudos UTHSC-SA!) and also 
OMOP.

They are looking for people to pilot the scripts 
https://github.com/ncats/CTSA-Metrics

Let Dr. Rosemond (cced) know if you want to pilot.

Erica: Maren Wennberg on our team at KUMC can run those for you.  Maren: can 
you check the scripts wrt if I should log it with the DROC as a feasibility or 
a DUA.  I think it’s just Counts and I don’t need to do a DUA.

Russ Waitman, PhD
Director of Medical Informatics
Associate Vice Chancellor for Enterprise Analytics Professor, Department of 
Internal Medicine University of Kansas Medical Center, Kansas City, Kansas
913-945-7087 (office)
rwait...@kumc.edu
http://www.kumc.edu/ea-mi/
http://informatics.kumc.edu
http://www.gpcnetwork.org
 – a PCORnet collaborative 
www.pcornet.org

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Re: Running CDM queries for CTSA program to calculate Common Metrics.

2017-09-01 Thread Taylor, Bradley

It’s just counts. I just ran it against our CDM and got results back. I do have 
a couple of questions though.

Regards,
Brad

Bradley W. Taylor
Chief Research Informatics Officer
Medical College of Wisconsin
Co-Director Biomedical Informatics
Clinical and Translational Science Institute
Site-PI PCORNet Greater Plains (GPC) CDRN
e: btay...@mcw.edu
p: 414-805-7307


From: Gpc-dev  on behalf of Russ Waitman 

Date: Friday, September 1, 2017 at 12:37 PM
To: "GPC-DEV@LISTSERV.KUMC.EDU" 
Cc: "'rosemo...@mail.nih.gov'" , "'clar...@uthscsa.edu' 
(clar...@uthscsa.edu)" 
Subject: Running CDM queries for CTSA program to calculate Common Metrics.

Hi Everyone,

You may already know this but I am on the CTSA call with the other sites and 
Erica Rosemond at NIH has worked with the San Antonio team to develop CTSA 
Informatics Common Metrics against the PCORnet CDM (kudos UTHSC-SA!) and also 
OMOP.

They are looking for people to pilot the scripts
https://github.com/ncats/CTSA-Metrics

Let Dr. Rosemond (cced) know if you want to pilot.

Erica: Maren Wennberg on our team at KUMC can run those for you.  Maren: can 
you check the scripts wrt if I should log it with the DROC as a feasibility or 
a DUA.  I think it’s just Counts and I don’t need to do a DUA.

Russ Waitman, PhD
Director of Medical Informatics
Associate Vice Chancellor for Enterprise Analytics
Professor, Department of Internal Medicine
University of Kansas Medical Center, Kansas City, Kansas
913-945-7087 (office)
rwait...@kumc.edu
http://www.kumc.edu/ea-mi/
http://informatics.kumc.edu
http://www.gpcnetwork.org
 – a PCORnet collaborative 
www.pcornet.org

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Running CDM queries for CTSA program to calculate Common Metrics.

2017-09-01 Thread Russ Waitman

Hi Everyone,

You may already know this but I am on the CTSA call with the other sites and 
Erica Rosemond at NIH has worked with the San Antonio team to develop CTSA 
Informatics Common Metrics against the PCORnet CDM (kudos UTHSC-SA!) and also 
OMOP.

They are looking for people to pilot the scripts
https://github.com/ncats/CTSA-Metrics

Let Dr. Rosemond (cced) know if you want to pilot.

Erica: Maren Wennberg on our team at KUMC can run those for you.  Maren: can 
you check the scripts wrt if I should log it with the DROC as a feasibility or 
a DUA.  I think it's just Counts and I don't need to do a DUA.

Russ Waitman, PhD
Director of Medical Informatics
Associate Vice Chancellor for Enterprise Analytics
Professor, Department of Internal Medicine
University of Kansas Medical Center, Kansas City, Kansas
913-945-7087 (office)
rwait...@kumc.edu
http://www.kumc.edu/ea-mi/
http://informatics.kumc.edu
http://www.gpcnetwork.org - a PCORnet collaborative 
www.pcornet.org

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

2017-09-01 Thread GPC Informatics

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by jmcclay):

 UNMC is aiming for the 8th to turn this around.

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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GPC NEXT-D Table1 request

2017-09-01 Thread Stoddard, Alexander


Updated code to run against Oracle CDM implementations for the NEXT-D table1 
subset request is available at: 
https://github.com/kumc-bmi/nextd-study-support/tree/master

I have updated the README to hopefully make clear how to run it.

Has a version of the query for SQLServer been worked on and/or is it available 
in the NextD Dropbox folders? I’d be happy to help with getting it added to the 
github repo.

Thank you,
Alex Stoddard
Biomedical Informatics Software Engineer
CTSI
414-805-7239

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RE: PCORI CDM Lab Issue

2017-09-01 Thread Verhagen, Laurel A

I'd love to hear what UW is doing, as they are at 100% for lab ranges. Debbie, 
can you help?

We were also dinged for this, but the problem may be different. The SCILHS ETL 
included normal ranges for selected labs. We may not have pulled the most 
recent version of i2p? The version we ran was limited to the shorter list of 
labs, not the newer direction to include all data. Our labs are stored with a 
local coding system that can be linked to LOINC. The challenge is that we have 
multiple local codes, with different ranges, for a single LOINC. Still looking 
into this...

Thanks,
Laurel

From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Phillip 
Reeder
Sent: Thursday, August 31, 2017 4:07 PM
To: gpc-dev@listserv.kumc.edu
Subject: PCORI CDM Lab Issue

Our CDM report showed us failing the check 3.10 for "LAB_NAME is a common 
measure* or LAB_LOINC is not null and RESULT_NUM is not null and 
NORM_MODIFIER_LOW, NORM_RANGE_LOW, NORM_MODIFIER_HIGH, and NORM_RANGE_HIGH are 
all populated per CDM specifications.**"

The difference between 3.09 and 3.10 seems to be the normal ranges, but we do 
have normal ranges in our data as we used the i2p code to generate the lab 
results.  Did anyone else have an issue like this with their last EDC report?  
Does anyone understand the SAS code well enough to help me figure out why this 
check was failing for us?

Thanks,
Phillip



UT Southwestern


Medical Center



The future of medicine, today.


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Please contact the sender and advise of the erroneous delivery by return e-mail 
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Re: PCORI CDM Lab Issue

2017-09-01 Thread Michael Prittie

Hi Phillip,
We ran into this issue at KUMC as well.  The i2p-tranform populates the normal 
range fields only if a LAB_NAME is defined for that specific lab, and does so 
with hard coded values curated by Harvard (which are likely different from the 
normal ranges are our sites).

Our short-term solution for Cycle 3 Refresh 1 to this was to build a LOINC-base 
lab normal range reference table based values provided by our hospital (you can 
view a diff of the changes 
here).  Our long-term 
solution is to pull per-lab normal range values into HERON (i2b2) from Epic 
Clarity and use those values when building the Lab_Result_CM table.

If you have any questions about this let me know.

Best,
Michael

From: Gpc-dev 
mailto:gpc-dev-boun...@listserv.kumc.edu>> 
on behalf of Phillip Reeder 
mailto:phillip.ree...@utsouthwestern.edu>>
Date: Thursday, August 31, 2017 at 4:06 PM
To: "gpc-dev@listserv.kumc.edu" 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: PCORI CDM Lab Issue

Our CDM report showed us failing the check 3.10 for "LAB_NAME is a common 
measure* or LAB_LOINC is not null and RESULT_NUM is not null and 
NORM_MODIFIER_LOW, NORM_RANGE_LOW, NORM_MODIFIER_HIGH, and NORM_RANGE_HIGH are 
all populated per CDM specifications.**”

The difference between 3.09 and 3.10 seems to be the normal ranges, but we do 
have normal ranges in our data as we used the i2p code to generate the lab 
results.  Did anyone else have an issue like this with their last EDC report?  
Does anyone understand the SAS code well enough to help me figure out why this 
check was failing for us?

Thanks,
Phillip



UT Southwestern


Medical Center



The future of medicine, today.

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Fw: PCORI CDM Lab Issue

2017-09-01 Thread Debbie Yoshihara


Hi,

A number of fields in CDM 3.1 changed in
precision.  Our engineer had this to say
about that:




PCORI CDM 3.1 Issues:



We had a couple issues that may be related as follows:

  *   Are they running the data_step_view_prep.sas first?  Probably yes… If 
yes, then just after the data_step_view_prep.sas completed and before any other 
sas jobs, open each data set and review the data in each field. Data errors 
will become apparent before running the rest of the sas jobs.Since PCORI 
changed the field lengths of some table fields there may be some SAS code that 
still assumes the old size of the table fields and therefore will truncate the 
data as is comes through the SAS views created by the data_step_view_prep.sas 
code. For LAB_RESULTS_CM table look in the data_step_view_prep.sas  for this 
table section and make the following change:

Result_num = input(result_num,best8.);  and change this to

Result_num = input(result_num,best32.8);

   And then re-run the data_step_view_prep.sas and review all the 
tables and fields values in SAS. In the SAS code anywhere where PCORI changed 
the field lengths potentially has this error.



 I’ve attached our data_step_view_prep.sas file for reference.





  *   The other issue to keep in mind relates to SAS Libraries. 
Data_step_view_prep.sas defines a libname called oracdata. Make sure in later 
SAS steps that you are not accidently re-defining this library in some other 
sas code.  You need to use the sas views created in data_step_view_prep.sas for 
the rest of the sas code in later steps.



Hope this helps.




From: Verhagen, Laurel A 
mailto:verhagen.lau...@marshfieldresearch.org>>
Sent: Friday, September 1, 2017 8:09 AM
To: Phillip Reeder; 
gpc-dev@listserv.kumc.edu; Debbie Yoshihara
Subject: RE: PCORI CDM Lab Issue



I’d love to hear what UW is doing, as they are at 100% for lab ranges. Debbie, 
can you help?



We were also dinged for this, but the problem may be different. The SCILHS ETL 
included normal ranges for selected labs. We may not have pulled the most 
recent version of i2p? The version we ran was limited to the shorter list of 
labs, not the newer direction to include all data. Our labs are stored with a 
local coding system that can be linked to LOINC. The challenge is that we have 
multiple local codes, with different ranges, for a single LOINC. Still looking 
into this…



Thanks,

Laurel



From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Phillip 
Reeder
Sent: Thursday, August 31, 2017 4:07 PM
To: gpc-dev@listserv.kumc.edu
Subject: PCORI CDM Lab Issue



Our CDM report showed us failing the check 3.10 for "LAB_NAME is a common 
measure* or LAB_LOINC is not null and RESULT_NUM is not null and 
NORM_MODIFIER_LOW, NORM_RANGE_LOW, NORM_MODIFIER_HIGH, and NORM_RANGE_HIGH are 
all populated per CDM specifications.**”



The difference between 3.09 and 3.10 seems to be the normal ranges, but we do 
have normal ranges in our data as we used the i2p code to generate the lab 
results.  Did anyone else have an issue like this with their last EDC report?  
Does anyone understand the SAS code well enough to help me figure out why this 
check was failing for us?



Thanks,

Phillip





UT Southwestern


Medical Center



The future of medicine, today.






The contents of this message may contain private, protected and/or privileged 
information. If you received this message in error, you should destroy the 
e-mail message and any attachments or copies, and you are prohibited from 
retaining, distributing, disclosing or using any information contained within. 
Please contact the sender and advise of the erroneous delivery by return e-mail 
or telephone. Thank you for your cooperation.


data_step_view_prep.sas
Description: data_step_view_prep.sas
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Re: PCORI CDM Lab Issue

2017-09-01 Thread Debbie Yoshihara

Hi,


We didn't do all labs, but I'll ask our

engineer what we did.  We didn't change

the code from last time.


--- Debbie


From: Verhagen, Laurel A 
Sent: Friday, September 1, 2017 8:09:49 AM
To: Phillip Reeder; gpc-dev@listserv.kumc.edu; Debbie Yoshihara
Subject: RE: PCORI CDM Lab Issue

I’d love to hear what UW is doing, as they are at 100% for lab ranges. Debbie, 
can you help?

We were also dinged for this, but the problem may be different. The SCILHS ETL 
included normal ranges for selected labs. We may not have pulled the most 
recent version of i2p? The version we ran was limited to the shorter list of 
labs, not the newer direction to include all data. Our labs are stored with a 
local coding system that can be linked to LOINC. The challenge is that we have 
multiple local codes, with different ranges, for a single LOINC. Still looking 
into this…

Thanks,
Laurel

From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Phillip 
Reeder
Sent: Thursday, August 31, 2017 4:07 PM
To: gpc-dev@listserv.kumc.edu
Subject: PCORI CDM Lab Issue

Our CDM report showed us failing the check 3.10 for "LAB_NAME is a common 
measure* or LAB_LOINC is not null and RESULT_NUM is not null and 
NORM_MODIFIER_LOW, NORM_RANGE_LOW, NORM_MODIFIER_HIGH, and NORM_RANGE_HIGH are 
all populated per CDM specifications.**”

The difference between 3.09 and 3.10 seems to be the normal ranges, but we do 
have normal ranges in our data as we used the i2p code to generate the lab 
results.  Did anyone else have an issue like this with their last EDC report?  
Does anyone understand the SAS code well enough to help me figure out why this 
check was failing for us?

Thanks,
Phillip



UT Southwestern


Medical Center



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