GPC Dev 5 Jan agenda and meeting notes

[Dan Connolly]

Happy New Year! What else for tomorrow?

MCW is scheduled to scribe
https://docs.google.com/document/d/1wwHZYjwKxj49aF_yZkAI-M2uiBiLnM8zovIxY64oFmc/edit

agenda snapshot:


  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
Zoom Meeting ID: 954 5765 9561 Passcode: 
357039

 *   Roll: GPC 
DevTeams 
represented? KUMC (chair), UIOWA, MCW (scribe), MCRI, UNMC, UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTHouston

 *   Comments on the agenda? On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   ref 
SoftwareDev#tracking

 *   Next meeting(s): Jan 19; scribe 
rotation:
 KUMC? UNMC?

*   Note preventable 
meeting at 
11:30 today and each 2nd, 4th Tue

  2.  Fw: CORRECTION: First COVID-19 Vaccine SCD Added
RXCUI: 
2468235 etc. FYI, right?

  3.  Jan refresh 
milestone:cdm-refresh-j21
 Distribution Date: Jan 4th, Results due: Jan 29

 *   Data Curation 
(beta)
 is available

  4.  
Milestone:tumor-reg-18

 *   opportunity to participate: cardiovascular outcomes of lung cancer 
tx

*   planning to participate: UTSW, MCRF, UTHSCSA

*   Unlikely: KUMC, Utah

*   Indiana: ?

 *   #749 
PCORNet style TUMOR 
table - progress to 
part of PCORNet CDM?

*   DC - will get back to JC on details of what he did previously in 
the next few days - In progress: Dec 11 value sets for TUMOR table from NAACCR 
tumor registry

  5.  
Milestone:snow-shrine-3
 - #411 
,#756 , ...

 *   Next meeting of ACT Data Harmonization 
Workgroup (not 
to be confused with i2b2/transmart Ontology work 
group Next 
ACT data harmonization meeting is Jan 4th; Ontology workgroup meeting will be 
December 17 10AM CST

 *   Ongoing discussion on who will be sponsoring nodes.



wash your hands 
… wear a 
mask and social distance.


--
Dan

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Re: GPC Dev 1 Dec agenda and meeting notes (hosted on Zoom)

[Dan Connolly]

I notice that several of you accepted a meeting invitation that looks like it 
was generated when I cancelled the KUMC hosting; that invitation ends in the 
past. I hope you also accepted the new invitation from MU.

In hopes of preempting any confusion about teleconference hosting:

  *   Zoom Meeting ID: 954 5765 9561 Passcode: 
357039<https://umsystemprotected.zoom.us/j/95457659561?pwd=TDg1dUZCbUFISDNqMFdqMUJsTjNDUT09>

https://umsystemprotected.zoom.us/j/95457659561?pwd=TDg1dUZCbUFISDNqMFdqMUJsTjNDUT09

From: Dan Connolly
Sent: Monday, November 30, 2020 12:07 PM
To: gpcde...@po.missouri.edu 
Cc: gpc-dev@listserv.kumc.edu 
Subject: GPC Dev 1 Dec agenda and meeting notes (hosted on Zoom)

What else for tomorrow?

MU is scheduled to scribe.
https://docs.google.com/document/d/18Jobjx7fOekLcRhbC_1Ptx9hbB8DKSqfKCQ15xY50YQ/edit

MU is also hosting the mailing list and teleconference now.
new: gpcde...@po.missouri.edu https://po.missouri.edu/cgi-bin/wa?A0=GPCDEV-L
old: gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/pipermail/gpc-dev/
please excuse any duplicates of this message.

agenda snapshot:


  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
Zoom Meeting ID: 954 5765 9561 Passcode: 
357039<https://umsystemprotected.zoom.us/j/95457659561?pwd=TDg1dUZCbUFISDNqMFdqMUJsTjNDUT09>

 *   Roll: GPC 
DevTeams<https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams> 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU (scribe), 
IndianaU, Utah, Allina, Intermountain, UTHouston

 *   Comments on the agenda? On last week’s notes? 
(#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12>)
Recent tickets 
opened/closed<https://informatics.gpcnetwork.org/trac/Project/timeline> - FYI 
(i.e. not intended for discussion)

*   ref 
SoftwareDev#tracking<https://informatics.gpcnetwork.org/trac/Project/wiki/SoftwareDev#tracking>

 *   Next meeting(s): Dec 8; scribe 
rotation<https://docs.google.com/document/d/1fPoDn0pdVvC-Mct58X7wkGD2rNiId8aNZ9JG_WCbcf4/edit#heading=h.zbjzupqx0rh7>:
 UIOWA? MCRI?

*   Time sharing with PREVENTABLE trial - stay tuned for invitation 
from MU / Deandra

*   Annette Wolfe / Nebraska: re metrics… I’m looking into a broader 
question of the metric calculation

*   #411<https://informatics.gpcnetwork.org/trac/Project/ticket/411> 
ACT SHRINE Ontology alignment - Data Harmonization 
Workgroup<https://dbmi-pitt.github.io/ACT-Network/data_harmonization.html> 
update since Apr 28? DC to schedule time when JRC is available

  2.  Jan refresh 
milestone:cdm-refresh-j21<https://informatics.gpcnetwork.org/trac/Project/milestone/cdm-refresh-j21>

 *   Hints on Trailing blanks fix in SAS from RDBMS.  Susan to send her 
methodology.

 *   beta testing; Checking LOINC codes whether lab observations or Obs 
Clin observations.  Alex to send a list of the LOINC codes they use (with no 
warranty of fitness…).

  3.  
Milestone:snow-shrine-3<https://informatics.gpcnetwork.org/trac/Project/milestone/snow-shrine-3>

 *   #767<https://informatics.gpcnetwork.org/trac/Project/ticket/767> GPC 
feasibility queries using ACT SHRINE 
network<https://informatics.gpcnetwork.org/trac/Project/ticket/767> - expansion 
beyond CTSA sites part of ACT renewal discussions? PR to ask around

 *   #756<https://informatics.gpcnetwork.org/trac/Project/ticket/756> 
Allina i2b2 ACT SHRINE 
node<https://informatics.gpcnetwork.org/trac/Project/ticket/756>


wash your hands 
…<https://www.cdc.gov/coronavirus/2019-ncov/prepare/prevention.html> wear a 
mask and social distance

--
Dan

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GPC Dev 1 Dec agenda and meeting notes (hosted on Zoom)

[Dan Connolly]

What else for tomorrow?

MU is scheduled to scribe.
https://docs.google.com/document/d/18Jobjx7fOekLcRhbC_1Ptx9hbB8DKSqfKCQ15xY50YQ/edit

MU is also hosting the mailing list and teleconference now.
new: gpcde...@po.missouri.edu https://po.missouri.edu/cgi-bin/wa?A0=GPCDEV-L
old: gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/pipermail/gpc-dev/
please excuse any duplicates of this message.

agenda snapshot:


  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
Zoom Meeting ID: 954 5765 9561 Passcode: 
357039

 *   Roll: GPC 
DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU (scribe), 
IndianaU, Utah, Allina, Intermountain, UTHouston

 *   Comments on the agenda? On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   ref 
SoftwareDev#tracking

 *   Next meeting(s): Dec 8; scribe 
rotation:
 UIOWA? MCRI?

*   Time sharing with PREVENTABLE trial - stay tuned for invitation 
from MU / Deandra

*   Annette Wolfe / Nebraska: re metrics… I’m looking into a broader 
question of the metric calculation

*   #411 
ACT SHRINE Ontology alignment - Data Harmonization 
Workgroup 
update since Apr 28? DC to schedule time when JRC is available

  2.  Jan refresh 
milestone:cdm-refresh-j21

 *   Hints on Trailing blanks fix in SAS from RDBMS.  Susan to send her 
methodology.

 *   beta testing; Checking LOINC codes whether lab observations or Obs 
Clin observations.  Alex to send a list of the LOINC codes they use (with no 
warranty of fitness…).

  3.  
Milestone:snow-shrine-3

 *   #767 GPC 
feasibility queries using ACT SHRINE 
network - expansion 
beyond CTSA sites part of ACT renewal discussions? PR to ask around

 *   #756 
Allina i2b2 ACT SHRINE 
node


wash your hands 
… wear a 
mask and social distance

--
Dan

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http://listserv.kumc.edu/mailman/listinfo/gpc-dev

Re: gpc-dev 24 Nov agenda and meeting notes

[Dan Connolly]

Thanks, Susan, for taking notes.

PDF copy attached for archiving and review.

I'm out of the habit of sending PDF copies, but during this mailing list 
archive transition, I figure it's worthwhile. Please excuse any duplicates in 
you inbox.

new: https://po.missouri.edu/cgi-bin/wa?A0=GPCDEV-L
old: http://listserv.kumc.edu/pipermail/gpc-dev/

--
Dan


From: Dan Connolly
Sent: Monday, November 23, 2020 11:24 AM
To: gpc-dev@listserv.kumc.edu 
Subject: gpc-dev 24 Nov agenda and meeting notes

What else for tomorrow?

Intermountain is scheduled to scribe
https://docs.google.com/document/d/1Tu6FdBmnJ-WjDo4DvfcfC2n1D3VhjJM0-glHbT_5ZI4/edit



  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381<https://global.gotomeeting.com/meeting/join/817393381>; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting<https://global.gotomeeting.com/meeting/join/817393381> preferences
GPC DevTeams<https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams> 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, IndianaU, 
Utah, Allina, Intermountain  (scribe), UTHouston

 *   Comments on the agenda? (ref 
SoftwareDev#tracking<https://informatics.gpcnetwork.org/trac/Project/wiki/SoftwareDev#tracking>)
 On last week’s notes? 
(#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12>)
Recent tickets 
opened/closed<https://informatics.gpcnetwork.org/trac/Project/timeline> - FYI 
(i.e. not intended for discussion)

*   None this week

*   S. Roush @ MCRI to provide response from DRNOC; done: Fw: GPC 
Network Progress Report Feedback and 
Questions<http://listserv.kumc.edu/pipermail/gpc-dev/2020q4/011122.html>

 *   Next meeting(s): Dec 1; scribe: MU? UIOWA?

*   MU / Zoom taking over conference hosting KUMC / Gotomeeting

*   Note scribe 
rotation<https://docs.google.com/document/d/1fPoDn0pdVvC-Mct58X7wkGD2rNiId8aNZ9JG_WCbcf4/edit#heading=h.zbjzupqx0rh7>
 appendix

*   Annette Wolfe / Nebraska: re metrics… I’m looking into a broader 
question of the metric calculation

  2.  Jan refresh 
milestone:cdm-refresh-j21<https://informatics.gpcnetwork.org/trac/Project/milestone/cdm-refresh-j21>

 *   beta testing; Full DCQ beta test became available on Monday 16 Nov.

 *   Hints on Trailing blanks fix in SAS from RDBMS.

*   Susan to send her methodology.

  3.  
Milestone:snow-shrine-3<https://informatics.gpcnetwork.org/trac/Project/milestone/snow-shrine-3>

 *   #411<https://informatics.gpcnetwork.org/trac/Project/ticket/411> ACT 
SHRINE Ontology alignment - Data Harmonization 
Workgroup<https://dbmi-pitt.github.io/ACT-Network/data_harmonization.html> 
update since Apr 28?

 *   #767<https://informatics.gpcnetwork.org/trac/Project/ticket/767> GPC 
feasibility queries using ACT SHRINE 
network<https://informatics.gpcnetwork.org/trac/Project/ticket/767>

 *   #756<https://informatics.gpcnetwork.org/trac/Project/ticket/756> 
Allina i2b2 ACT SHRINE 
node<https://informatics.gpcnetwork.org/trac/Project/ticket/756> - RW is no 
longer in the ACT meetings since transition to MU



wash your hands 
…<https://www.cdc.gov/coronavirus/2019-ncov/prepare/prevention.html> wear a 
mask and social distance


--
Dan



24 Nov gpc-dev meeting notes.pdf
Description: 24 Nov gpc-dev meeting notes.pdf
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trailing blanks in SAS

[Dan Connolly]

Hi Susan,

In our Nov 10 meeting when Alex reported struggles with trailing blanks in SAS, 
you offered to share some code. If you already sent it, I must have missed it. 
Help me find it?

It's fine if what you have is not a complete solution.

--
Dan

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Canceled: GPC Dev Weekly Teleconference

[Dan Connolly]

BEGIN:VCALENDAR
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ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=gpc-dev@li
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Osinski, K
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Donglu Xie
 :MAILTO:donglu@utsouthwestern.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Tamara Win
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Wright,  M
 ichael J":MAILTO:michael-wrigh...@uiowa.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Brooklyn W
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Hood, Dani
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Gassner, C
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Russ Waitm
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Scotty, Er
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Nathan Hen
 sel:MAILTO:nhen...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Hillary Sa
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Imran Hafe
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ATTACH:CID:11D705C9DEB9CB408D442D6ABD5FCE76@kumc.edu
DESCRIPTION;LANGUAGE=en-US:\nA meeting agenda is due to the gpc-dev mailing
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 r more information see:\n<https://informatics.gpcnetwork.org/trac/Project/
 wiki/SoftwareDev#next-agenda>https://informatics.gpcnetwork.org/trac/Proje
 ct/wiki/SoftwareDev\n\n\nWhen: Occurs every Tuesday from 11:00 AM to 12:00
  PM\, effective 9/25/18-12/31/19. (UTC-06:00) Central Time (US & Canada)\n
 \n  1.  Please join my meeting: https://global.gotomeeting.com/meeting/joi
 n/817393381\n  2.  Use your microphone and speakers (VoIP) - a headset is 
 recommended. Or\, call in using your telephone.\n  United States (Toll-fre
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GPC Dev Weekly Teleconference

[Dan Connolly]

BEGIN:VCALENDAR
METHOD:REQUEST
PRODID:Microsoft Exchange Server 2010
VERSION:2.0
BEGIN:VTIMEZONE
TZID:Central Standard Time
BEGIN:STANDARD
DTSTART:16010101T02
TZOFFSETFROM:-0500
TZOFFSETTO:-0600
RRULE:FREQ=YEARLY;INTERVAL=1;BYDAY=1SU;BYMONTH=11
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RRULE:FREQ=YEARLY;INTERVAL=1;BYDAY=2SU;BYMONTH=3
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BEGIN:VEVENT
ORGANIZER;CN=Dan Connolly;SENT-BY="MAILTO:gpc-dev-boun...@listserv.kumc.edu":
 MAILTO:dconno...@kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=gpc-dev@li
 stserv.kumc.edu:MAILTO:gpc-dev@listserv.kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Osinski, K
 risten":MAILTO:kosin...@mcw.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Donglu Xie
 :MAILTO:donglu@utsouthwestern.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Tamara Win
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Wright,  M
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Brooklyn W
 inkel:MAILTO:bwink...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Hood, Dani
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Xing Song:
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Gassner, C
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Russ Waitm
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Scotty, Er
 ica J":MAILTO:scotty.er...@marshfieldresearch.org
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Nathan Hen
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Hillary Sa
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Imran Hafe
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 urs every Tuesday from 11:00 AM to 12:00 PM\, effective 9/25/18-12/31/19. 
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gpc-dev 24 Nov agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

Intermountain is scheduled to scribe
https://docs.google.com/document/d/1Tu6FdBmnJ-WjDo4DvfcfC2n1D3VhjJM0-glHbT_5ZI4/edit



  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, IndianaU, 
Utah, Allina, Intermountain  (scribe), UTHouston

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

*   S. Roush @ MCRI to provide response from DRNOC; done: Fw: GPC 
Network Progress Report Feedback and 
Questions

 *   Next meeting(s): Dec 1; scribe: MU? UIOWA?

*   MU / Zoom taking over conference hosting KUMC / Gotomeeting

*   Note scribe 
rotation
 appendix

*   Annette Wolfe / Nebraska: re metrics… I’m looking into a broader 
question of the metric calculation

  2.  Jan refresh 
milestone:cdm-refresh-j21

 *   beta testing; Full DCQ beta test became available on Monday 16 Nov.

 *   Hints on Trailing blanks fix in SAS from RDBMS.

*   Susan to send her methodology.

  3.  
Milestone:snow-shrine-3

 *   #411 ACT 
SHRINE Ontology alignment - Data Harmonization 
Workgroup 
update since Apr 28?

 *   #767 GPC 
feasibility queries using ACT SHRINE 
network

 *   #756 
Allina i2b2 ACT SHRINE 
node - RW is no 
longer in the ACT meetings since transition to MU



wash your hands 
… wear a 
mask and social distance


--
Dan

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Fw: GPC Network Progress Report Feedback and Questions

[Dan Connolly]

Wow.. the mailing list widget really doesn't like you, does it, Steffani?

Hm... it looks like you sent to gpc-dev-boun...@listserv.kumc.edu ; the normal 
place to send is gpc-dev@listserv.kumc.edu .

Anyway... thanks for getting this info!

--
Dan



From: Roush, Steffani 
Sent: Tuesday, November 17, 2020 11:29 AM
To: gpc-dev-boun...@listserv.kumc.edu 
Subject: GPC Network Progress Report Feedback and Questions

Hi Everyone,

Here are our questions/concerns regarding the network progress report and 
DRNOC's responses:

Concerns with how metrics are calculated:

* Shut downs in health systems due to COVID-19 affected data latency/patient 
counts in the March-April timeframe. Is this still being counted against sites? 
If not, can DRNOC address this concern?
o DRNOC: We understand and see that pattern at many sites. We provided PCORI 
that context to keep in mind as they review the data.

* Query responsiveness metrics are being calculated based on the date the query 
was approved vs. when the query was returned. Does it still count against sites 
if they return a query on time but it is not reviewed/approved by DRNOC until 
after the due date? What about instances where the queries were returned on 
time, but there was an issue identified (error in log or wrong attachment 
sent)? Sites do not feel this should be counted against them.
o DRNOC: Metrics on if a data curation submission was "on time" is from when an 
"approvable" package was submitted, not when it was approved. So if a site 
submits their response on the due date, and there are no issues, they are 
counted as on time even if the approval email does not go out for a few days. 
However, if the site responds on the due date with issues that must be 
remediated, they are considered late until the respond with a package that has 
no issues.
o SLR: Requesting clarification on this line from item above: However, if the 
site responds on the due date with issues that must be remediated, they are 
considered late until the respond with a package that has no issues. Does this 
mean that if a site turns around revised query responses after the due date, 
their response is not counted as late?
o DRNOC: Query response metrics are based on when the site responds.

* PRO CM Table not populated - Additional guidance on this table would be 
appreciated. Without studies that explicitly use this table it is hard to 
justify populating for some sites. Populating this table requires months of 
work for data that is not otherwise leveraged.
o DRNOC: PCORI requested feedback on the population of all tables and we 
provided them context as to why certain tables may be less prioritized by sites 
to participate.

* Obs Gen and Obs Clin Tables not populated - comments similar to the statement 
above. Dev team acknowledges that obs clin will be populated from here on out 
due to the deprecation of the vitals table.
o See above


General Comments

*  Responsiveness to PopMedNet queries: It would be helpful if naming 
conventions between this report and what is seen in the Datamart Client were 
consistent. It is hard to match up what is represented here to what was 
submitted otherwise.
o DRNOC: Noted

* Network Studies: it would be helpful to have PI listed. It is hard to keep 
track of which study is which in this report. One example is the BP Control 
study listed on page 7. There are multiple BP studies going on in the network 
at the same time and it's hard to differentiate in this report.
o DRNOC: This section is being updated and will have all 3 Aims of BP control 
in next report.

* General comment: A dashboard that is updated regularly (weekly?) with this 
information would be helpful. Sites would like to see how they are scoring 
during the reporting period so that issues can be addressed if needed.
o DRNOC: Please see iMeet for QI reports that are updated ~monthly and as needed
o Link: https://pcornet.imeetcentral.com/pcornetbenchmarks/doc/WzIsNDg1Mzc5NjVd/
o Additional Info: Query metrics that are found on iMeet are based on site 
responding by the due date with data in final report. So both criteria need to 
be met, which doesn't fully align with Progress Report Metrics.



Steffani Roush
Research Programmer Analyst Senior | Office of Research Computing and Analytics
Marshfield Clinic Research Institute
Office: 715-221-6442 | Ext: 1-6442


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gpc-dev 10 Nov agenda and meeting notes

[Dan Connolly]

Anything else for tomorrow? I'm planning to keep the meeting to 30 min.

Indiana is scheduled to scribe.
https://docs.google.com/document/d/1aOcJFV2fTl0HEgWAeY9neZnNQPR8hnW9QyxXaN92l9U/edit

agenda snapshot:

  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, IndianaU 
(scribe), Utah, Allina, Intermountain, UTHouston

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Nov 17; scribe: MU? Utah?

*   Note scribe 
rotation
 appendix

  2.  FW: [External] PCORnet Weekly Announcement - October 29th, 2020 
   Gryzlak, 
Brian M

  3.  Performance Report - clarifications about what counts as approved, e.g. 
in case of resubmissions.

 *   S. Roush @ MCRI to provide response from DRNOC

 *   Annette Wolfe / Nebraska: re metrics… I’m looking into a broader 
question of the metric calculation

  4.  Jan refresh 
milestone:cdm-refresh-j21

 *   MCW is beta testing

  5.  i2b2 tranSMART events: 2020 European 
Virtual Symposium


wash your hands 
… wear a 
mask and social distance

--
Dan

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gpc-dev 3 Nov agenda and meeting notes

[Dan Connolly]

I didn't find much in the way of agenda; any suggestions?

UTSW was scheduled to scribe Oct 27; are you available tomorrow?
https://docs.google.com/document/d/1zd8YdaXoNB5-uc0l5Ky3fjUz7WWWZldeTb4yo7EHMNI/edit


logistics:

11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

--
Dan



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gpc-dev 20 Oct agenda and meeting notes

[Dan Connolly]

Let's do meet today. Please excuse the delay in preparing an agenda.

I neglected to recruit a scribe last week. Next in rotation are UTHSCSA? UTSW?

https://docs.google.com/document/d/18sWA9Z79pEvhM-xI6v_ryCb5_WvJjnVr4p4SR72yV3M/edit

logistics:


  1.  Convene, take roll, review records and plan the next meeting(s).

11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

--
Dan

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large national cohort study that relates to COVID-19 in children, adolescents, and /or young adults.

[Dan Connolly]

Russ writes:
Could you share on a gpc-dev call tomorrow to see how the network views 
responses to these questions.  Basically not extensive analysis but a best 
estimate.
It's not entirely clear to me what sites should estimate in tomorrow's call. 
patient counts? Or effort to collect the counts? I suppose you'll be there to 
clarify, Russ...

And I presume we'll see a DROC request before sites are expected to share 
counts.

--
Dan



NICHD RFI Form via Kleinman.docx
Description: NICHD RFI Form via Kleinman.docx
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gpc-dev 13 Oct agenda and meeting notes

[Dan Connolly]

Anything else for tomorrow?

Allina is scheduled to scribe.
https://docs.google.com/document/d/11DNaadVc3Iv60ZPD53V4jQHDfrgIQCgmzqL7hucvGg0/edit

agenda snapshot:

  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, IndianaU, 
Utah, Allina (scribe), Intermountain, UTHouston

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
763notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Oct 20; scribe: UTHSCSA? UTSW?

*   Note scribe 
rotation
 appendix

  2.  PCORNet CDM Cycle 8, Third Refresh DC 
v5.13?
 5 Oct distribution; 26 Oct results due
Ref 2020 Data Curation Queries from ​DRNOC Forum July 
2020

 *   Approved: Utah

 *   UNMC at moderate risk for 26 Oct

  3.  Performance Report Russ Waitman: Sent to PIs, gpc project management 
group.

 *   UTSW & Intermountain question - what does approved mean? Do we have 
control over that? If we submit on time and then resubmit - is that a “ding”. 
Marshfield - please reach out to DRN OC for more detail


wash your hands 
… wear a 
mask and social distance

--
Dan

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gpc-dev 6 Oct agenda and meeting notes

[Dan Connolly]

What else for tomorrow?
For reference, I cc'd Russ at his new MU address.

UNMC is scheduled to scribe.
https://docs.google.com/document/d/1Tab0znPmj8A6ecIjLGGleWkJWExXp9fF3H7VFJZG8C4/edit

agenda snapshot:

  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC (scribe), UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTHouston

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
763notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   #749 (PCORNet style TUMOR table) 
closed

 *   Next meeting(s): Oct 13; scribe: Allina?, UTHSCSA?

*   Note scribe 
rotation
 appendix

  2.  GPC DROC Request Submission #85 
   mwennberg at 
kumc.edu

 *   Cell size restriction?, revised code Oct 
2

  3.  PCORNet CDM Cycle 8, Third Refresh DC 
v5.13?
 5 Oct distribution; 26 Oct results due
Ref 2020 Data Curation Queries from ​DRNOC Forum July 
2020

 *   UNMC at moderate risk for 26 Oct

 *   Performance report card. Sent to PIs, gpc project management group.
Due 7 Oct to Deandra. Meeting 23 Oct

wash your hands 
… wear a 
mask and social distance

--
Dan

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gpc-dev 29 Sep agenda and meeting notes

[Dan Connolly]

What else for today's meeting?

KUMC is scheduled to scribe.
https://docs.google.com/document/d/18XVjBZvbPuJSLl2GLuFhpk7XrCAFwX_-pEq5BqeSPIc/edit

agenda snapshot, including the usual logistics details:

  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair, scribe), UIOWA, MCW, MCRI, UNMC (regrets JRC), 
UTHSCSA, UTSW, MU, IndianaU, Utah, Allina, Intermountain, UTH

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
763notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   #765 (get volume / quality threshold for Sentinel participation) 
created

*   #766 (DeathDataSharing - document license / justification change) 
created

 *   Next meeting(s): Oct 6; scribe: Allina? UNMC?

*   Note scribe 
rotation
 appendix

*   #759 
covid19 PCORNet 
datamarts: PHII 
(contracting group for CDC) is waiting for their award. 15 Sep + ~3 weeks?

  2.  PCORNet CDM Cycle 8, Third Refresh DC 
v5.13?
 5 Oct distribution; 26 Oct results due
Ref 2020 Data Curation Queries from ​DRNOC Forum July 
2020

 *   FW: CDM v6 draft specification for comment 
   Russ Waitman
Laura, Alex to review and send email to GPC dev. Done:

*   CDM 6.0 review responses from MCW 
   Stoddard, 
Alexander

*   CDM 6.0 review responses from MCW 
   Manuel, Laura 
S M

 *   UNMC at risk for 26 Oct

 *   Performance reports [?]

  3.  
Milestone:tumor-reg-18

 *   #749 
PCORNet style TUMOR 
table - 
kumc-bmi/naaccr-tumor-data
#760
 duplicates in tumor table: collect data from 
sites - DROC 
Request 
#82
 - SAS code for DROC #82
Build a TUMOR 
table, run SAS code and return results to 
https://redcap.kumc.edu/surveys/?s=PC3Y8DXNTH
any technique to get it into the form specified in tumor 
table.version1.2.xlsx
 is sufficient.

*   Submitted: UIOWA, UTHSCSA, MCW

*   (UNMC, Utah, Allina, Intermountain not expected to participate for 
reasons given in earlier meetings.)

*   KUMC - DC: to see that this gets done - at risk

*   MCRI -  submitted last week

*   Indiana - Jeff   ETA mid-late Sept - Tony F.

*   UTSW - PR: Changed update to merge; ready to submit in the next few 
days (after 8 Sep) - still in progress - no update

*   MU - Will look at the code from MCW and ask questions as needed, 
query received, work not started

  4.  #411 Nebraska 
lexicon update
UNMC to send the updated ontology (RxNorm, SNOMED-CT, LOINC, ICD-10CM) to MCW, 
and Intermountain


wash your hands 
… wear a 
mask and social distance

--
Dan

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gpc-dev 22 Sep agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

MCW is scheduled to scribe.
https://docs.google.com/document/d/1pd1qChbJ4Hs2LWkh2V8YcsSzgyWIRjbtflNlvqYGvz8/edit

current agenda snapshot:

  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW (scribe), MCRI, UNMC, UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
763notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   #765 (get volume / quality threshold for Sentinel participation) 
created

*   #766 (DeathDataSharing - document license / justification change) 
created

 *   Next meeting(s): Sep 29; scribe: Allina? KUMC?

*   Note scribe 
rotation
 appendix

*   #759 
covid19 PCORNet 
datamarts: PHII 
(contracting group for CDC) is waiting for their award. 15 Sep + ~3 weeks?

  2.  PCORNet CDM Cycle 8, Third Refresh DC 
v5.13?
 5 Oct distribution; 26 Oct results due
Ref 2020 Data Curation Queries from ​DRNOC Forum July 
2020

 *   FW: CDM v6 draft specification for comment 
   Russ Waitman
Solicit 2 reviewers to start GPC’s review

  3.  
Milestone:tumor-reg-18

 *   #749 
PCORNet style TUMOR 
table - 
kumc-bmi/naaccr-tumor-data
#760
 duplicates in tumor table: collect data from 
sites - DROC 
Request 
#82
 - SAS code for DROC #82
Build a TUMOR 
table, run SAS code and return results to 
https://redcap.kumc.edu/surveys/?s=PC3Y8DXNTH
any technique to get it into the form specified in tumor 
table.version1.2.xlsx
 is sufficient.

*   Submitted: UIOWA, UTHSCSA, MCW

*   (UNMC, Utah, Allina, Intermountain not expected to participate for 
reasons given in earlier meetings.)

*   KUMC - DC: to see that this gets done

*   MCRI -  Will be submitting this week

*   Indiana - Jeff   ETA mid-late Sept - Tony F.

*   UTSW - PR: Changed update to merge; ready to submit in the next few 
days (after 8 Sep) - still in progress

*   MU - Will look at the code from MCW and ask questions as needed

  4.  #411 Nebraska 
lexicon update
UNMC to send the updated ontology (RxNorm, SNOMED-CT, LOINC, ICD-10CM) to MCW, 
and Intermountain



wash your hands 
… wear a 
mask and social distance

--
Dan

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gpc-dev 15 Sep agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

Marshfield is scheduled to scribe.
https://docs.google.com/document/d/1N3Z0coOHGrc1mXDodKpEWSzycBgtwxSuBiTlcznnrVs/edit

current agenda snapshot:


  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI (scribe), UNMC, UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
763notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None; one new ticket is under next-d below

 *   Next meeting(s): Sep 22; scribe: MCW? Allina?

*   Note scribe 
rotation
 appendix

*   FW: Sentinel next steps in PCORnet 
   Russ Waitman 
Jul 1
Dan/KUMC to get more info about volume / quality issues where the line was 
divided (not immediately)

  2.  2020 Data Curation Queries from ​DRNOC Forum July 2020
Cycle
 8, Third Refresh DC 
v5.13?
 5 Oct distribution; 26 Oct results due

 *   Follow up on the Data WG Meeting 7/17 
  “Is there any 
interest to characterize more lab results data to see how well the ABN_IND 
performs to fill gaps where there are not normal ranges?” S. Rea and/or S. 
Roush to coordinate with DRN OC; Sep 14 forum?

  3.  #411 Nebraska 
lexicon update: Release notes still show 20170331. News since gpc-dev meetings 
in April 2020?

  4.  
Milestone:next-d

 *   #763 NEXTD: FACILITY_TYPE & PROVIDER_SPECIALTY
Goal is to ensure 
the Oct refresh has this issue addressed and then submit to NEXT-D out of the 
approved Oct refresh.

*   UTSW - Easier to submit NPIs

*   MCW - generated mapping between dept id (internal to MCW) and fac 
type (the latter is PCORnet generated).

*   KUMC - DC to report more on KUMC’s efforts next week. done:

   *   “current approach only populated 20% Need to do more 
investigation.” -- XS 12 
Sep

*   UNMC - JRC will investigate into facility type issue

*   IU - Dan Hood will check with analyst on status

*   UIOWA - Mark C to check into facility type

 *   #764 (DM medications 4 DM patients) created by A'lona 
Furmanchuck

*   Alona to review diabetic med code lists from Jim C @ UNMC via DC. 
done.

*   Iowa -

*   Indiana -

*   UNMC -

  5.  
Milestone:covid19wk

 *   #759 
covid19 PCORNet 
datamarts: PHII 
(contracting group for CDC) is waiting for their award. ~3 weeks?

  6.  
Milestone:tumor-reg-18

 *   #749 
PCORNet style TUMOR 
table - 
kumc-bmi/naaccr-tumor-data
#760
 duplicates in tumor table: collect data from 
sites - DROC 
Request 
#82
 - SAS code for DROC #82
Build a TUMOR 
table, run SAS code and return results to 
https://redcap.kumc.edu/surveys/?s=PC3Y8DXNTH
any technique to get it into the form specified in tumor 

gpc-dev 8 Sep agenda and meeting notes

[Dan Connolly]

 I trust you all enjoyed the holiday weekend. Input to today's agenda is 
welcome.

UIOWA is scheduled to scribe.
https://docs.google.com/document/d/1XU9-8SpOIXymFp1GOtwtIbEP_yQLnMj0ZPePe0pi63k/edit


  1.  Convene, take roll, review records, and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA (scribe), MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

 *   Comments on the agenda?

 *   Next meeting(s): Sep 15; scribe: ???

  2.  stuff from last week 
(#12)

  3.  stuff from tickets by 
milestone

  4.  stuff from ​gpc-dev email

  5.  new/closed/reopened 
tickets


--
Dan

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gpc-dev Sep 1 agenda and meeting notes

[Dan Connolly]

What else for today? I haven't spent much time looking for things that changed 
in the last week...

--
Dan



From: Dan Connolly
Sent: Monday, August 24, 2020 3:39 PM
To: gpc-dev@listserv.kumc.edu 
Subject: gpc-dev Aug 25 agenda and meeting notes

What else for tomorrow?

Intermountain is scheduled to scribe.
https://docs.google.com/document/d/1D7AgAmKNSg249kunB7eVADsfH69YEqkajt3Cmsniorw/edit

agenda snapshot:

  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381<https://global.gotomeeting.com/meeting/join/817393381>; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting<https://global.gotomeeting.com/meeting/join/817393381> preferences
GPC DevTeams<https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams> 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, IndianaU, 
Utah, Allina, Intermountain  (scribe), UTH

 *   Comments on the agenda? (ref 
SoftwareDev#tracking<https://informatics.gpcnetwork.org/trac/Project/wiki/SoftwareDev#tracking>)
 On last week’s 
notes?<https://docs.google.com/document/d/1D7AgAmKNSg249kunB7eVADsfH69YEqkajt3Cmsniorw/edit#heading=h.9ioc8gnd1ijp>
 (#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12>)
Recent tickets 
opened/closed<https://informatics.gpcnetwork.org/trac/Project/timeline> - FYI 
(i.e. not intended for discussion)

*   #762 (Peer review of Houston’s PCORNet CDM) 
created<https://informatics.gpcnetwork.org/trac/Project/ticket/762>

 *   Next meeting(s): Sep 1; scribe: UIOWA? MCRI?

*   Note scribe 
rotation<https://docs.google.com/document/d/1fPoDn0pdVvC-Mct58X7wkGD2rNiId8aNZ9JG_WCbcf4/edit#heading=h.zbjzupqx0rh7>
 appendix

*   FW: Sentinel next steps in PCORnet 
<http://listserv.kumc.edu/pipermail/gpc-dev/2020q3/011005.html>   Russ Waitman 
Jul 1
Dan/KUMC to get more info about volume / quality issues where the line was 
divided (not immediately)

*   
DeathDataSharing<https://informatics.gpcnetwork.org/trac/Project/wiki/DeathDataSharing>
 - license / justification
DC: UIOWA asked Dec 
2019<https://informatics.gpcnetwork.org/trac/Project/ticket/688#comment:18> - 
answer was private communication from RW.
DC to follow up with Deandra - in progress

  2.  2020 Data Curation Queries from ​DRNOC Forum July 
2020<https://pcornet.imeetcentral.com/drnoc-workgroups/folder/WzIwLDEyOTgxNzU1XQ/WzIsNzEzMTYxNjld/>

 *   Lab characterization v1 - debrief
10 Aug query distribution; 24 Aug results due

 *   Cycle 8, Third Refresh DC v5.13?
5 Oct distribution; 26 Oct results due

  3.  
Milestone:covid19wk<https://informatics.gpcnetwork.org/trac/Project/milestone/covid19wk>

 *   #759<https://informatics.gpcnetwork.org/trac/Project/ticket/759> 
covid19 PCORNet datamarts
<https://informatics.gpcnetwork.org/trac/Project/ticket/759>funding is via CDC 
directly to individual sites; Aug 5 to PMs; 6 GPC sites; not KUMC, MU, UTSW 
unless additional funding. - News?

  4.  
Milestone:tumor-reg-18<https://informatics.gpcnetwork.org/trac/Project/milestone/tumor-reg-18>
 aiming for Jul 10

 *   #749<https://informatics.gpcnetwork.org/trac/Project/ticket/749> 
PCORNet style TUMOR 
table<https://informatics.gpcnetwork.org/trac/Project/ticket/749> - 
kumc-bmi/naaccr-tumor-data
<https://github.com/kumc-bmi/naaccr-tumor-data>#760<https://informatics.gpcnetwork.org/trac/Project/ticket/760>
 duplicates in tumor table: collect data from 
sites<https://informatics.gpcnetwork.org/trac/Project/ticket/760> - DROC 
Request 
#82<https://redcap.kumc.edu/redcap_v9.5.25/DataEntry/index.php?pid=16659=82_id=44812=gpc_droc_oversight_request>
 - SAS code for DROC 
#82<http://listserv.kumc.edu/pipermail/gpc-dev/2020q3/011046.html>

*   Brad to follow up with Brian / Maren re Where to submit

*   Brad/Brian: Is September 1 to have a TUMOR table, run SAS code and 
return results realistic?

   *   UIOWA - done

   *   UTHSCSA - All set to submit

   *   KUMC - 1 Sep looks feasible

   *   MCRF - 1 Sep seems feasible, yes.

   *   MCW - 1 Sep is possible but risky

   *   Indiana - Jeff will spend ~1hr trying 
kumc-bmi/naaccr-tumor-data<https://github.com/kumc-bmi/naaccr-tumor-data>

   *   UTSW - still testing code.  July 14th is the latest JAR file.

  *   DC to look into patient_mapping using item 2300 MRN

   *   MU -  1 Sep at risk, at best

   *   (UNMC - maybe in the future.)

   *   (Utah - Not currently able to participate. Access to tumor 
registry still in progress.)

   *   Allina - Need more time than 1 Sep

   *   (Intermountain - still working thru organizational issues to get 
a

Re: [External] DROC 82 Tumor Table Mapping

[Dan Connolly]

It was semi-conscious. That is: I asked about it (July 
7) and 
you said OK, but I doubt you realized the impact.

Also noted as https://github.com/kumc-bmi/naaccr-tumor-data/issues/19

--
Dan


From: Gpc-dev  on behalf of McDowell, 
Bradley D 
Sent: Friday, August 28, 2020 1:07 PM
To: Osinski, Kristen ; gpc-dev@listserv.kumc.edu 

Subject: RE: [External] DROC 82 Tumor Table Mapping


Hi Kris,



That’s interesting… NAACCR has always had these three redundant fields for 
ICD-O-2, and you might have the same issue for the ICD-O-3 fields as well 
(numbers 521-523). It appears that 419 and 521 remain part of the NAACCR 
dictionary, but we did not include them in the tumor table. (I honestly can’t 
recall if that was a conscious decision.) I wonder if your institution’s tumor 
registry decided to populate 419 only and leave 420 and 430 blank since they’re 
redundant.



Could you split your morphology variable into separate histology and behavior 
values and use those to populate 420 and 430? The first four characters 
correspond to histology and the last character corresponds to behavior 
(separated by a “/”).



Thanks!



Brad



From: Osinski, Kristen 
Sent: Friday, August 28, 2020 12:03 PM
To: gpc-dev@listserv.kumc.edu
Cc: McDowell, Bradley D 
Subject: [External] DROC 82 Tumor Table Mapping



Hi Brad,

I have found what may be a versioning mismatch in our NAACCR table vs. your 
Version 18 model for DROC 82. We have mappings for NAACCR Item 419 
[Morph--Type ICD-O-2 ] but the new version appears to have broken Item 
419 into 2 separate variables for Histology Type (420) and Behavior (430). Do 
you have a preference on which new variable I should map our Item 419 data to?



Best,

Kris

(414) 416-2389 (cell)



Kristen Osinski, MS

Business Analyst, Biomedical Informatics

Clinical & Translational Science Institute, Suite M1350

Medical College of Wisconsin

8701 Watertown Plank Road

Milwaukee, WI 53226

kosin...@mcw.edu (414) 805-7245



[signature_491657025][signature_46665966]

Please cite the NIH CTSA Grant; 2UL1TR001436, 2TL1TR001437, 2KL2TR001438, and 
acknowledge support.


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Re: PCORNet Tumor table

[Dan Connolly]

All the configuration goes in the db.properties file, just like with i2b2 ("in 
section 3.4.2 Set Database 
Properties<https://community.i2b2.org/wiki/display/getstarted/3.4.2+Set+Database+Properties>
 of the i2b2 installation 
guide<https://community.i2b2.org/wiki/display/getstarted/i2b2+Installation+Guide>")

You shouldn't need to change any of the .groovy files.

Oh... the README probably should talk about db.properties by name in that 
section, shouldn't it? Sorry.

It's documented down in the reference section, but that's pretty obscure:


 --db=PROPS database properties file [default: db.properties]

--
Dan


From: mrkfw 
Sent: Thursday, August 27, 2020 9:52 AM
To: Dan Connolly ; Mandhadi, Vasanthi (Medical Research 
Office) ; gpc-dev@listserv.kumc.edu 

Subject: Re: PCORNet Tumor table


Hi,



According to the “Getting Started” section of README, we need to modify/provide 
the Database configuration, naccr.flat-file and, i2b2.patient-mapping-query and 
then generate the jar file.



In “DBConfig.groovy” file, we could modify the Database configuration, but we 
are not sure where to modify or provide the  naccr.flat-file and 
i2b2.patient-mapping-query.



This is my understanding so far, please correct me if I am wrong and provide a 
guidance accordingly.



Thank you,

Rana



From: Dan Connolly 
Date: Wednesday, August 26, 2020 at 11:04 AM
To: "Mandhadi, Vasanthi (Medical Research Office)" 
, "gpc-dev@listserv.kumc.edu" 

Cc: mrkfw 
Subject: Re: PCORNet Tumor table



Yes, that's the right documentation and jar file*.



Does the "Getting Started" section of the README make sense?



*for the jar file, the commit hash is not part of its URL:

https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.7.4/naaccr-tumor-data.jar<https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.7.4/naaccr-tumor-data.jar>



--

Dan







From: Gpc-dev  on behalf of Mandhadi, 
Vasanthi (Medical Research Office) 
Sent: Wednesday, August 26, 2020 10:12 AM
To: gpc-dev@listserv.kumc.edu 
Cc: mrkfw 
Subject: PCORNet Tumor table



Hi GPC-dev,



We are starting to look into implementing the pcornet tumor table from NAACCR 
tumor data. I am not sure if I am looking at the latest readme file and jar 
file that other sites used. If not can anyone share the correct jar file and 
instructions.



ReadMe: 
https://github.com/kumc-bmi/naaccr-tumor-data#readme<https://github.com/kumc-bmi/naaccr-tumor-data#readme>

Jar file: 
https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.4-pcornet-1/naaccr-tumor-data.jar<https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.4-pcornet-1/naaccr-tumor-data.jar>1342e39



Any suggestions or guidance on how to get started would be helpful.



Thank you,

Vasanthi Mandhadi

Sr. Research Design Engineer

University of Missouri School of Medicine

Office: (573) 882-6273

Cell: (573) 529-8151


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Re: PCORNet Tumor table

[Dan Connolly]

Yes, that's the right documentation and jar file*.

Does the "Getting Started" section of the README make sense?

*for the jar file, the commit hash is not part of its URL:
https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.7.4/naaccr-tumor-data.jar

--
Dan



From: Gpc-dev  on behalf of Mandhadi, 
Vasanthi (Medical Research Office) 
Sent: Wednesday, August 26, 2020 10:12 AM
To: gpc-dev@listserv.kumc.edu 
Cc: mrkfw 
Subject: PCORNet Tumor table


Hi GPC-dev,



We are starting to look into implementing the pcornet tumor table from NAACCR 
tumor data. I am not sure if I am looking at the latest readme file and jar 
file that other sites used. If not can anyone share the correct jar file and 
instructions.



ReadMe: https://github.com/kumc-bmi/naaccr-tumor-data#readme

Jar file: 
https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.4-pcornet-1/naaccr-tumor-data.jar1342e39



Any suggestions or guidance on how to get started would be helpful.



Thank you,

Vasanthi Mandhadi

Sr. Research Design Engineer

University of Missouri School of Medicine

Office: (573) 882-6273

Cell: (573) 529-8151


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gpc-dev Aug 25 agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

Intermountain is scheduled to scribe.
https://docs.google.com/document/d/1D7AgAmKNSg249kunB7eVADsfH69YEqkajt3Cmsniorw/edit

agenda snapshot:

  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, IndianaU, 
Utah, Allina, Intermountain  (scribe), UTH

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   #762 (Peer review of Houston’s PCORNet CDM) 
created

 *   Next meeting(s): Sep 1; scribe: UIOWA? MCRI?

*   Note scribe 
rotation
 appendix

*   FW: Sentinel next steps in PCORnet 
   Russ Waitman 
Jul 1
Dan/KUMC to get more info about volume / quality issues where the line was 
divided (not immediately)

*   
DeathDataSharing
 - license / justification
DC: UIOWA asked Dec 
2019 - 
answer was private communication from RW.
DC to follow up with Deandra - in progress

  2.  2020 Data Curation Queries from ​DRNOC Forum July 
2020

 *   Lab characterization v1 - debrief
10 Aug query distribution; 24 Aug results due

 *   Cycle 8, Third Refresh DC v5.13?
5 Oct distribution; 26 Oct results due

  3.  
Milestone:covid19wk

 *   #759 
covid19 PCORNet datamarts
funding is via CDC 
directly to individual sites; Aug 5 to PMs; 6 GPC sites; not KUMC, MU, UTSW 
unless additional funding. - News?

  4.  
Milestone:tumor-reg-18
 aiming for Jul 10

 *   #749 
PCORNet style TUMOR 
table - 
kumc-bmi/naaccr-tumor-data
#760
 duplicates in tumor table: collect data from 
sites - DROC 
Request 
#82
 - SAS code for DROC 
#82

*   Brad to follow up with Brian / Maren re Where to submit

*   Brad/Brian: Is September 1 to have a TUMOR table, run SAS code and 
return results realistic?

   *   UIOWA - done

   *   UTHSCSA - All set to submit

   *   KUMC - 1 Sep looks feasible

   *   MCRF - 1 Sep seems feasible, yes.

   *   MCW - 1 Sep is possible but risky

   *   Indiana - Jeff will spend ~1hr trying 
kumc-bmi/naaccr-tumor-data

   *   UTSW - still testing code.  July 14th is the latest JAR file.

  *   DC to look into patient_mapping using item 2300 MRN

   *   MU -  1 Sep at risk, at best

   *   (UNMC - maybe in the future.)

   *   (Utah - Not currently able to participate. Access to tumor 
registry still in progress.)

   *   Allina - Need more time than 1 Sep

   *   (Intermountain - still working thru organizational issues to get 
access to the tumor registry data.)

 *   #739 HERON 
NAACCR ETL outdated by 
v18 
kumc-bmi/naaccr-tumor-data

*   DC to look into patient_mapping using item 2300 MRN


wash your hands 
… 

gpc-dev 28 Aug agenda and meeting notes

[Dan Connolly]

agenda is in progress

Intermountain is scheduled to scribe
https://docs.google.com/document/d/19fcbBd4xJsKH3mkkqyKDxYxpaN0OMI5x-yAPv34suag/edit


  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

--
Dan

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gpc-dev 11 Aug agenda and meeting notes

[Dan Connolly]

Today's agenda is in progress; please excuse the delay.

MU is scheduled to scribe.
https://docs.google.com/document/d/1S9iKXo8nd-pe03qSrnqewLcgWlaWvPNeylVeo_hWOF4/edit


  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

--
Dan

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Re: Follow up on the Data WG Meeting 7/17

[Dan Connolly]

Ah. OK. I understand now.

From: Keith Marsolo 
Sent: Monday, August 3, 2020 1:19 PM
To: Dan Connolly 
Cc: Mei Liu ; Russ Waitman ; 
gpc-dev@listserv.kumc.edu 
Subject: Re: Follow up on the Data WG Meeting 7/17

Hi Dan.

The purpose of the lookup table is to handle those results where the range is 
not part of the record itself.  Many clinical labs maintain a table or catalog 
of ranges.  The idea would be to have the lookup table capture that 
information.  But we wouldn’t go the other direction.  We wouldn’t try to 
reverse engineer the range based on what’s stored within the individual 
records.  If a record has a range and a unit, that’s sufficient.

Thanks.

Keith


On Aug 3, 2020, at 2:09 PM, Dan Connolly 
mailto:dconno...@kumc.edu>> wrote:

Hi Kieth and company,

I think the concern here is that at a site like Intermountain, there are N lab 
systems, and building one normal range metadata table to rule them all is 
somewhere between a large engineering project and an open research project.

Given that we already have LAB_RESULT_CM.NORM_RANGE_LOW and 
LAB_RESULT_CM.NORM_RANGE_HIGH for the the widespread practice where normal 
ranges come out of the lab systems with each result, why is it essential to 
build a table with some compressed version of those data?

--
Dan


From: Gpc-dev 
mailto:gpc-dev-boun...@listserv.kumc.edu>> 
on behalf of Mei Liu mailto:mei...@kumc.edu>>
Sent: Monday, August 3, 2020 9:01 AM
To: Russ Waitman mailto:rwait...@kumc.edu>>; 
gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu> 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: FW: Follow up on the Data WG Meeting 7/17

Please see the following email for DRONC’s response regarding our concerns and 
questions with the CDM lab normal range table.



Thanks,



Mei



From: Keith Marsolo mailto:keith.mars...@duke.edu>>
Sent: Thursday, July 30, 2020 12:10 PM
To: Mei Liu mailto:mei...@kumc.edu>>
Subject: Re: Follow up on the Data WG Meeting 7/17
Importance: High



Hi Mei.



We ask for all labs for a couple of reasons.  The first is that it allows us to 
get a sense of the “universe” of lab data across the PCORnet, and allows us to 
track the network’s improvement in mapping labs to LOINC.  The second reason is 
that we get requests from outside investigators / sponsors about potential 
projects that require lab data.  Through the data curation results, we can 
determine which sites have records using LOINC codes, and having all labs 
allows us to look at the RAW_NAME to determine if the records are potentially 
available and just not mapped.  Going forward, we’ve been working with the NLM 
on queries to better assess the quality of lab data mappings, which will be 
more effective if applied to all labs.



For the 2nd question, it’s really about normal ranges and units.  We can’t 
really query lab data without units, because while we could potentially guess 
at the unit, we’d have to trust that the LOINC code is correct, and we still 
discover instances where labs have incorrect LOINC codes.  With normal ranges, 
we haven’t done a ton of work with them yet because we’re still relatively new 
at querying labs, but they can be very helpful in assigning thresholds or cut 
points.  Many vary by age/race/gender, so understanding that site-level 
variation is helpful during analysis.



Hope that helps.  Let me know if there are other questions.



Keith




On Jul 27, 2020, at 10:54 AM, Mei Liu mailto:mei...@kumc.edu>> 
wrote:



Hi Keith,



After the Data WG meeting on 7/17, GPC sites had an internal discussion on the 
feasibility of creating a reference range look-up table for labs. Our major 
concern is that it may not be feasible for sites like Intermountain Health and 
IU/Regenstrief in our network to create such table because they have numerous 
hospitals that use different lab facilities resulting in inconsistent lab 
normal ranges. Intermountain had a unique case where their central lab lost a 
section of historic normal range data when they upgraded software, resulting in 
78% complete on normal ranges whereas their usual coverage of Lab Normal ranges 
for quantitative labs is ~95%. So, that gap will fill in and completeness 
should be back above 80% over time.



GPC sites would like the DRNOC to clarify the following two questions:

  1.  Since we have been asked to dump all lab data into CDM, it would be 
useful if the DRNOC could articulate why it seems useful – or have they found 
it useful in practice – to ask for every site’s entire lab data holdings.
  2.  Why are these Lab Normal tables in the CDM needed?



Thank you!



Mei
-
Mei Liu, PhD
Associate Professor
Department of Internal Medicine
Division of Medical Informatics
University of Kansas Medical Center
Office: 913-945-6446
Fax: 913-588-4880

_

Re: Follow up on the Data WG Meeting 7/17

[Dan Connolly]

Hi Kieth and company,

I think the concern here is that at a site like Intermountain, there are N lab 
systems, and building one normal range metadata table to rule them all is 
somewhere between a large engineering project and an open research project.

Given that we already have LAB_RESULT_CM.NORM_RANGE_LOW and 
LAB_RESULT_CM.NORM_RANGE_HIGH for the the widespread practice where normal 
ranges come out of the lab systems with each result, why is it essential to 
build a table with some compressed version of those data?

--
Dan


From: Gpc-dev  on behalf of Mei Liu 

Sent: Monday, August 3, 2020 9:01 AM
To: Russ Waitman ; gpc-dev@listserv.kumc.edu 

Subject: FW: Follow up on the Data WG Meeting 7/17


Please see the following email for DRONC’s response regarding our concerns and 
questions with the CDM lab normal range table.



Thanks,



Mei



From: Keith Marsolo 
Sent: Thursday, July 30, 2020 12:10 PM
To: Mei Liu 
Subject: Re: Follow up on the Data WG Meeting 7/17
Importance: High



Hi Mei.



We ask for all labs for a couple of reasons.  The first is that it allows us to 
get a sense of the “universe” of lab data across the PCORnet, and allows us to 
track the network’s improvement in mapping labs to LOINC.  The second reason is 
that we get requests from outside investigators / sponsors about potential 
projects that require lab data.  Through the data curation results, we can 
determine which sites have records using LOINC codes, and having all labs 
allows us to look at the RAW_NAME to determine if the records are potentially 
available and just not mapped.  Going forward, we’ve been working with the NLM 
on queries to better assess the quality of lab data mappings, which will be 
more effective if applied to all labs.



For the 2nd question, it’s really about normal ranges and units.  We can’t 
really query lab data without units, because while we could potentially guess 
at the unit, we’d have to trust that the LOINC code is correct, and we still 
discover instances where labs have incorrect LOINC codes.  With normal ranges, 
we haven’t done a ton of work with them yet because we’re still relatively new 
at querying labs, but they can be very helpful in assigning thresholds or cut 
points.  Many vary by age/race/gender, so understanding that site-level 
variation is helpful during analysis.



Hope that helps.  Let me know if there are other questions.



Keith





On Jul 27, 2020, at 10:54 AM, Mei Liu mailto:mei...@kumc.edu>> 
wrote:



Hi Keith,



After the Data WG meeting on 7/17, GPC sites had an internal discussion on the 
feasibility of creating a reference range look-up table for labs. Our major 
concern is that it may not be feasible for sites like Intermountain Health and 
IU/Regenstrief in our network to create such table because they have numerous 
hospitals that use different lab facilities resulting in inconsistent lab 
normal ranges. Intermountain had a unique case where their central lab lost a 
section of historic normal range data when they upgraded software, resulting in 
78% complete on normal ranges whereas their usual coverage of Lab Normal ranges 
for quantitative labs is ~95%. So, that gap will fill in and completeness 
should be back above 80% over time.



GPC sites would like the DRNOC to clarify the following two questions:

  1.  Since we have been asked to dump all lab data into CDM, it would be 
useful if the DRNOC could articulate why it seems useful – or have they found 
it useful in practice – to ask for every site’s entire lab data holdings.
  2.  Why are these Lab Normal tables in the CDM needed?



Thank you!



Mei

-

Mei Liu, PhD

Associate Professor

Department of Internal Medicine

Division of Medical Informatics

University of Kansas Medical Center

Office: 913-945-6446

Fax: 913-588-4880


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gpc-dev 21 July agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UTHSCSA is scheduled to scribe
https://docs.google.com/document/d/18NSOQU1dKCc6Hzv_-TpJQnNQ_TBo-zs5Af1AfXH051Y/edit


  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA (scribe), UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Jul 28; scribe: UTSW?, IU?

*   Note scribe 
rotation
 appendix

*   #759 
covid19 PCORNet 
datamarts 28 May 
“pause additional ETL development” until PCORI completes its review… Russ 
standing by for more info

*   Dan/KUMC to get more info about volume / quality issues where the 
line was divided (not immediately)

*   Marshfield will submit Bardet-Biedl Syndrome request through DROC

  2.  PCORnet CDM refresh with 
PPRL - due July 27

 *   C4UI r024 
Approved gold 
star!

  3.  
Milestone:tumor-reg-18
 aiming for Jul 10

 *   #749 
PCORNet style TUMOR 
table

*   Brian to update gpc-dev w.r.t. DROC request

 *   #739 HERON 
NAACCR ETL outdated by 
v18 
kumc-bmi/naaccr-tumor-data

*   DC to look into patient_mapping using item 2300 MRN

  4.  1228 covid query due July 21
PR: what’s expected, given May 28 “pause additional ETL development”?
Steph to ask DRNOC to clarify.
DC to confirm Russ is attending today’s PCORnet steering committee meeting and 
suggest that he seek clarification. Done: 1228 covid query due July 21? 
   Block, Jason 
Perry,M.D.


wash your hands 
...

--
Dan

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SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request [was: gpc-dev July 14 agenda]

[Dan Connolly]

From: Roush, Steffani 
Sent: Monday, July 13, 2020 12:42 PM
To: Dan Connolly 
Subject: RE: gpc-dev July 14 agenda and meeting notes


Hi Dan,



Can you add something to the agenda for me? I would add it myself, but MCHS IS 
recently revoked my access to google docs, and I’m still trying to get an 
internet override request approved…



Topic:



Bardet-Biedel Syndrome (BBS) Request

·Dr. VanWormer and Dr. Haws at Marshfield are looking to put in a 
proposal for a study relating to BBS

·Numbers are needed from GPC to see if we have sufficient population

o   ICD 9/10 codes are too vague and not specific to this condition

o   There is a SNOMED code (5619004) specific to BBS that may potentially be 
used

§  Do sites in GPC fill their Condition and Diagnosis CDM tables with SNOMED 
codes?

§  If not, how difficult would it be for sites to identify the number of 
patients with this condition using document searches/NLP?

·Ideas needed for getting these counts from all of PCORnet

o   If sites have this SNOMED code in their CDM then this will be much easier 
to accomplish than if sites need to use NLP



Thanks,





[image006]Steffani Roush

Research Programmer Analyst Senior | Office of Research Computing and Analytics

Marshfield Clinic Research Institute

Office: 715-221-6442 | Ext: 1-6442



From: Gpc-dev  On Behalf Of Dan Connolly
Sent: Monday, July 13, 2020 10:15 AM
To: gpc-dev@listserv.kumc.edu
Subject: [EXTERNAL] gpc-dev July 14 agenda and meeting notes



CAUTION: This email originated from outside of the Marshfield Clinic Health 
System. Do not click links or open attachments unless you recognize the sender 
and know the content is safe.




What else for tomorrow?



UNMC is scheduled to scribe

https://docs.google.com/document/d/1Bs0kkY7wI9SPZnmQBHEg9lfNDzuS-T2M_MJoT-aAajk/edit<https://urldefense.com/v3/__https:/docs.google.com/document/d/1Bs0kkY7wI9SPZnmQBHEg9lfNDzuS-T2M_MJoT-aAajk/edit__;!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyDrFiwfB$>



agenda snapshot:



1. Convene, take roll, review records and plan the next meeting(s).

a. 11:00 a.m. Central Time.
Meeting ID and access code: 
817-393-381<https://urldefense.com/v3/__https:/global.gotomeeting.com/meeting/join/817393381__;!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyOTIPTTa$>;
 call +1 (571) 317-3131

b. Roll; Reminder - put site after your name in 
GoToMeeting<https://urldefense.com/v3/__https:/global.gotomeeting.com/meeting/join/817393381__;!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyOTIPTTa$>
 preferences
GPC 
DevTeams<https://urldefense.com/v3/__https:/informatics.gpcnetwork.org/trac/Project/wiki/DevTeams__;!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyNbZFZ-q$>
 represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC (scribe), UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

c. Comments on the agenda? (ref 
SoftwareDev#tracking<https://urldefense.com/v3/__https:/informatics.gpcnetwork.org/trac/Project/wiki/SoftwareDev*tracking__;Iw!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyOZkII2e$>)
 On last week’s 
notes?<https://urldefense.com/v3/__https:/docs.google.com/document/d/1Bs0kkY7wI9SPZnmQBHEg9lfNDzuS-T2M_MJoT-aAajk/edit*heading=h.9ioc8gnd1ijp__;Iw!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyH0ZeCSv$>
 
(#12<https://urldefense.com/v3/__https:/informatics.gpcnetwork.org/trac/Project/ticket/12__;!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyO21kJx6$>)
Recent tickets 
opened/closed<https://urldefense.com/v3/__https:/informatics.gpcnetwork.org/trac/Project/timeline__;!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyJXJaqMM$>
 - FYI (i.e. not intended for discussion)

   i.  None this week

d. Next meeting(s): Jul 21; scribe: UTHSCSA? UTSW?

.  Note scribe 
rotation<https://urldefense.com/v3/__https:/docs.google.com/document/d/1fPoDn0pdVvC-Mct58X7wkGD2rNiId8aNZ9JG_WCbcf4/edit*heading=h.zbjzupqx0rh7__;Iw!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyN75KaDw$>
 appendix

   i.  
#759<https://urldefense.com/v3/__https:/informatics.gpcnetwork.org/trac/Project/ticket/759__;!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyBCkkOur$>
 covid19 PCORNet 
datamarts<https://urldefense.com/v3/__https:/informatics.gpcnetwork.org/trac/Project/ticket/759__;!!J7HzeEKFbK9hUUY!ZYyAOc-AfdFaspfIf4FEFoJNGge_p2C0Ht_OMEykQueEMZnM4OwkcXQoqLNh36ElfbxOyBC

gpc-dev July 14 agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UNMC is scheduled to scribe
https://docs.google.com/document/d/1Bs0kkY7wI9SPZnmQBHEg9lfNDzuS-T2M_MJoT-aAajk/edit

agenda snapshot:


  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC (scribe), UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Jul 21; scribe: UTHSCSA? UTSW?

*   Note scribe 
rotation
 appendix

*   #759 
covid19 PCORNet 
datamarts pause 
additional ETL development until PCORI completes its review… Russ standing by 
for more info

*   Dan/KUMC to get more info about volume / quality issues where the 
line was divided (not immediately)

  2.  PCORnet CDM refresh with 
PPRL - due July 27

  3.  
Milestone:tumor-reg-18
 aiming for Jul 10

 *   #749 
PCORNet style TUMOR 
table

*   To appear: release of 
kumc-bmi/naaccr-tumor-data with 
support for multiple files 
(#26), v16 
(#43)

 *   #739 HERON 
NAACCR ETL outdated by 
v18



wash your hands 
...


--
Dan

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gpc-dev Jul 6 agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

KUMC is scheduled to scribe.
https://docs.google.com/document/d/1XE6aYYWS8eNhtlWCc_3y4kL9cd6KgwXIdJh74baRnZc/edit

Agenda snapshot:

  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair, scribe), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

*   #759 
covid19 PCORNet 
datamarts pause 
additional ETL development until PCORI completes its review… Russ standing by 
for more info

 *   Next meeting(s): Jul 14; scribe: UNMC? UTHSCSA?

*   Note scribe 
rotation
 appendix

  2.  PCORnet CDM refresh - query scheduled to arrive Jul 3 Jul 6; due July 27

  3.  GPC DROC Request Submission #79 
   mwennberg at 
kumc.edu

  4.  FW: Sentinel next steps in PCORnet 
   Russ Waitman

  5.  
Milestone:tumor-reg-18
 aiming for Jul 10

 *   #739 HERON 
NAACCR ETL outdated by 
v18

 *   #749 
PCORNet style TUMOR 
table

  6.  
milestone:snow-shrine-3

 *   #411 DC 
sending SR rxnorm metadata.zip to Susan @ Intermountain - send started

 *   #756 
Allina i2b2 ACT SHRINE 
node - what news 
since Mar 19? Does Russ still have the ball?



wash your hands 
...

--
Dan

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Re: GPC Request #77, Dr. Brixner COVID Counts

[Dan Connolly]

Maren, I see UTSW submitted data for this. That's all I had pending on the 
gpc-dev agenda, so I'm leaving this off tomorrow's agenda unless I hear 
otherwise.

--
Dan


From: Gpc-dev  on behalf of Maren Lowrance 

Sent: Tuesday, June 23, 2020 11:06 AM
To: 'gpc-d...@listserv.kumc.edu' ; 
gpc-dev@listserv.kumc.edu 
Subject: GPC Request #77, Dr. Brixner COVID Counts


Dear GPC-DROC and GPC-DEV members,

As a reminder, please review and submit counts for Request # 77 
[redcap.kumc.edu]

  *   Requestor: Diana Brixner
  *   GPC's Datamart Feasibility Query (counts only)
  *   Title: Evaluation of a National COVID-19 Clinical Records Database to 
Explore Differences in Treatment and Outcomes for Vulnerable Populations
  *   Deadline: 06-24-2020
  *   Sites still missing DROC review and/or data submission:
 *   Indiana
 *   Intermountain
 *   Iowa
 *   UTHSCA
 *   UTSW
  *   Submission Link: https://redcap.kumc.edu/surveys/?s=W7FF4HJ7EY



Thank you,



Maren Lowrance

Assistant Director of Product Design and Analysis

GPC Honest Broker

University of Kansas Medical Center

913-588-7688




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gpc-dev 23 Jun agenda and meeting notes

[Dan Connolly]

Please excuse the delay; I was out yesterday.

MCW is scheduled to scribe
https://docs.google.com/document/d/1mZR0XvEh0JRZdff6avic9pqDsvyRyGVAVhmoqRTPKB0/edit

11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

--
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gpc-dev 9 Jun agenda and meeting notes

[Dan Connolly]

What else for tomorrow? I found just a few things but they seem worth a short 
meeting.

Intermountain is scheduled to scribe
https://docs.google.com/document/d/1LjxSYeJFeeAhdwNrzXAoACslKS6spEG_jItGScmt1fU/edit

agenda snapshot:


 1.  Convene, take roll, review records and plan the next meeting(s).

*   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

*   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, IndianaU, 
Utah, Allina, Intermountain (scribe), UTH

*   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

   *   None this week

*   Next meeting(s): Jun 16; scribe: Marshfield? MCW?

   *   Note scribe 
rotation
 appendix

 2.  
Milestone:tumor-reg-18

*   #760 (duplicates in tumor table: collect data from sites)
#749
 PCORNet style TUMOR 
table

   *   Cancer CRG is requesting real dates to conduct quality control work; 
Brad/Brian has the ball - UIOWA will present on the Gov call tomorrow (6/3)

   *   UIOWA used R code to create the NAACCR table.
Done: R script for NAACCR to PCORnet tumor table 
   Gryzlak, 
Brian M

   *   DC to ... prepare demonstration for gpc-dev - slipped another 2 weeks

 3.  
milestone:covid19wk

*   #759 
covid19 PCORNet 
datamarts

   *   PCORnet 2.0 Steering Committee Meeting 5/26: … pause additional ETL 
development until PCORI completes its review…
Russ may get more info Jun 2

 4.  #411 Jim C - 
offered to share RxNorm metadata from last i2b2 build with KUMC - done.


wash your hands 
...

--
Dan

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gpc-dev 2 Jun agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UIOWA is scheduled to scribe:
https://docs.google.com/document/d/1b2YUTZdYvtAezYwZt_5ilbqvHTRFuMaYkmeouKAEb2Y/edit

agenda snapshot:


 1.  Convene, take roll, review records and plan the next meeting(s).

*   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

*   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA (scribe), MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

*   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

   *   None this week

*   Next meeting(s): Jun 9; scribe: MCRF? Intermountain?

   *   Note scribe 
rotation
 appendix

 2.  
Milestone:tumor-reg-18

*   #739 HERON 
NAACCR ETL outdated by 
v18

   *   HERON release this week

   *   kumc-bmi/naaccr-tumor-data
May 15 release 
v0.4-pcornet-1
 
1342e39

   *   UTSW: Current version does not work on pre-v18.
#43 v16 fails with NaaccrIOException: invalid line 
length 
bug

*   #749 
PCORNet style TUMOR 
table

*   #760 (duplicates in tumor table: collect data from 
sites)

   *   UIOWA used R code to create the NAACCR table.  Will share shortly.

   *   DC to ... prepare demonstration for gpc-dev

 3.  
milestone:covid19wk

*   #759 
covid19 PCORNet 
datamarts

   *   Waitman Tuesday, May 26, 2020 at 1:22 PM in re PCORnet 2.0 Steering 
Committee Meeting 5/26:
For COVID CDM (slide 33), note you can pause additional ETL development until 
PCORI completes its review of the supplements and they are also in discussion 
with further input from CDC.


wash your hands 
...

--
Dan

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gpc-dev 25 May agenda and meeting notes

[Dan Connolly]

Welcome back from the holiday. As a result, I don't have a detailed agenda yet.

Utah is scheduled to scribe
https://docs.google.com/document/d/1NmbAFrlaiSfXSOPviTHUw1856SMpzQ-gbOreafc3wOk/edit


  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, IndianaU, 
Utah (scribe), Allina, Intermountain, UTH

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): ...

  2.  @

  3.  stuff from last week 
(#12)

  4.  stuff from tickets by 
milestone

  5.  stuff from ​gpc-dev email

  6.  new/closed/reopened 
tickets


--
Dan

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KUMC COVID i2b2 & Data Informational Session (May 8, 2020)

[Dan Connolly]

FYI, some materials from a recent presentation at KUMC are available:

 *   COVID Data 
Resources
 - KUMC Medical Informatics

Thanks to Maren, Song, and Noor for presenting the work of our group so well.

Maren, we didn't already announce this to gpc-dev, did we?

--
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gpc-dev 19 May agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

MU is scheduled to scribe
https://docs.google.com/document/d/1bjBEk9b9PdtZIu5zLW8sWWesVY6O-1M4tU4C8pZl_Sk/edit

agenda snapshot:

 1.  Convene, take roll, review records and plan the next meeting(s).

*   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

*   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU (scribe), 
IndianaU, Utah, Allina, Intermountain, UTH

*   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

   *   None this week

*   Next meeting(s): May 26; scribe: Utah? UIowa?

   *   Note scribe 
rotation
 appendix

 2.  PPRL / DataVant 
/ Common Linkage for July refresh
per slide 3 of 20200505 PCORnet Steering Committee slides

*   “Sites with COVID-related complications that might affect this timeline 
should notify the PMO by May 15, 2020.”

 3.  
Milestone:tumor-reg-18

*   #739 HERON 
NAACCR ETL outdated by v18
v0.3-electric-beta
 
cc28f83

*   #749 
PCORNet style TUMOR 
table

   *   BM to send DROC request - limited data, IRB...

   *   DC to test naaccr-tumor-data.jar vs. Brad’s specs. Done; “we just 
have a few name mismatches due to some recent renaming”

   *   DC to meet with Jay @ UNMC to test further and prepare demonstration 
for gpc-dev call. Done:
README
https://github.com/kumc-bmi/naaccr-tumor-data/releases/download/v0.4-pcornet-1/naaccr-tumor-data.jar
 1342e39

 4.  
milestone:covid19wk
 4th query due May 4

*   #759 
covid19 PCORNet 
datamarts

   *   Ryan C. to share with working group that distribution of these 
documents need to be shared via a wider list.

*   #758 
covid19 ACT nodes refreshed 
2x/week

   *   new ACT Derived 
Variables
 spreadsheet
Dan to follow up on pregnancy and immunocompromised derived variables. (in 
progress) (both 
sheets.)

 5.  #411 UNMC to 
refresh medication RXNorm and NDC metadata and make available


wash your hands 
...

--
Dan

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titles of COVID docs on imeetcentral from last week's notes

[Dan Connolly]

Steffani, help?

I'm trying to clean up last week's notes. I'd like to make it clear which of 
these documents is what. Would you please give me the titles? (bonus point for 
date and author)

https://pcornet.imeetcentral.com/pcornet20folderwziwldewodeymzc1xq/folder/WzIwLDEyNzY0MjQ5XQ/
https://pcornet.imeetcentral.com/drnoc-workgroups/folder/WzIwLDEyODU5MzkyXQ/WzIsNzA1MjkxMzZd/
https://pcornet.imeetcentral.com/pcornet20folderwziwldewodeymzc1xq/folder/WzIwLDEyODU3MDcyXQ/

When I try to access them, I get:

You are not authorized to access the system in the manner you were attempting.


--
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gpc-dev 5 May agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UTSW is scheduled to scribe
https://docs.google.com/document/d/1g4i2VLsf-dwt2fzEbB3OhzgItqa0caVpdlh0M0ImO-o/edit

agenda snapshot:

  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW (scribe), MU, 
IndianaU, Utah, Allina, Intermountain, UTH

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): May 12; scribe: MU? IU?

*   Note scribe 
rotation
 appendix

  2.  Apr 2020 PCORnet CDM refresh: due Apr 27

 *   Done: KUMC (Submitted), 
UIOWA, 
MCW, 
MCRF, 
UNMC, 
UTHSCSA, 
UTSW, 
MU, 
Utah, 
IndianaU, 
Allina, 
Intermountain

 *   UTH- Checking

  3.  
milestone:covid19wk
 4th query due May 4

 *   #759 
covid19 PCORNet 
datamarts

*   Susan Rea: Will send that [LOINC Code for the COVID-19 antigen 
testing that is not on the list that PCORI is using]. 
(done)

*   CDM+ in May for COVID19? revised 
SOW Apr 20
final SOW was sent out by Deandra. Review and response by May 11th

 *   #758 
covid19 ACT nodes refreshed 
2x/week

*   new ACT Derived 
Variables
 spreadsheet
Dan to follow up on pregnancy and immunocompromised derived variables. (in 
progress)

 *   #411 Jim 
Campbell: should have medication RXNorm and NDC meta data available for use 
within another week or two.

  4.  SS Death 
Sharing 
and Welcome UT Houston!

 *   KUMC to distribute to UTH (along with others) by ~12 May

  5.  
Milestone:tumor-reg-18

 *   #739 HERON 
NAACCR ETL outdated by v18
v0.3-electric-beta
 cc28f83
DC
 to merge onejar to master (done)

 *   #749 
PCORNet style TUMOR table
tumor table 
   McDowell, 
Bradley D


wash your hands 
...

--
Dan

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Re: tumor table

[Dan Connolly]

Interesting... can you point us to the materials that the Cancer CRG developed?

I'm still working with the design I shared March 19.
https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/749/tumor_data.sql

I haven't worked on the duplicate issue but I included it in a list of 
pcornet-related issues
https://github.com/kumc-bmi/naaccr-tumor-data/labels/pcornet


--
Dan


From: Gpc-dev  on behalf of McDowell, 
Bradley D 
Sent: Friday, May 1, 2020 7:51 AM
To: '' 
Subject: tumor table




Quick summary: We’re looking for volunteer sites to implement the PCORnet tumor 
table and provide case-level data on potential duplicates.



Hello everyone,



The PCORnet Cancer Collaborative Research Group developed a tumor table that 
was approved by the PCORnet Data Committee as an optional addition to the CDM. 
We have been working with the table here at the University of Iowa before 
widely disseminating the specifications. These experiences have led to several 
improvements, and they have also motivated us to deal with one of the central 
problems with the underlying institutional tumor registry data: duplicate 
records. Registries often generate multiple records for the same tumor when new 
case information is found, and these records are hard to distinguish from true 
multiple primary cancers. This problem has had serious implications for two GPC 
studies that used the tumor registry data.



Using data from the UI tumor registry, we have developed guidance for dealing 
duplicate records. It is difficult to know, however, if this guidance only 
applies to UI data or if there are other problems that will reveal themselves 
when other sites implement the tumor table specifications. We are looking for 
sites to volunteer to:



  1.  Implement the tumor table and provide feedback to the Cancer CRG
  2.  Run a SAS query that will provide data on potential duplicate records. 
The query will generate a case listing to share with the Cancer CRG that 
identifies differing values across records for the same patient. This will be 
used to develop further guidance for dealing with duplicate records and improve 
the GPC data infrastructure; it will not be used for research.



An optional DROC request will be forthcoming, but I wanted to send this message 
in advance to see if there were any concerns. Please contact me if you have any 
questions or if you might be interested in participating. I’m happy to talk 
about this at our weekly conference call if that would be helpful.



Thank you,



Brad




Bradley D. McDowell, Ph.D.
Director, Population Research Core
Holden Comprehensive Cancer Center



5240 MERF | The University of Iowa | Iowa City, IA | 52242
Office: 319-384-1768


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ACT Derived Variables: how?

[Dan Connolly]

Lav, did you and Maren just update our Covid ETL to handle the new ACT Derived 
Variables
 spreadsheet? How did we do it? Point me / us to the code or whatever?


ref:
gpc-dev 28 Apr agenda and meeting 
notes

Phillip Reeder: There’s a new ACT Derived 
Variables
 spreadsheet; e.g. immunocompromised. How are others doing the derived 
variables? Some talk about them being in flowsheets. Fear if we’re all pulling 
things different ways the results will be different because it’s not the same 
thing to pull from billing vs flowsheets
Pregnancy and other things are also being added in.
DC: Pregnancy is derived?
PR: It wasn’t based off the ICD code.
Jim McClay: Pregnancy can be a derived variable… especially with time 
constraints around the pandemic
PR: I plan to bring it up on the ACT Code as a need to standardize how we are 
deriving it, but if others could also push for standardization that would be 
appreciated.
Dan to follow up on pregnancy and immunocompromised derived variables.

--
Dan


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gpc-dev 28 Apr agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UTHSCSA is scheduled to scribe
https://docs.google.com/document/d/10K5iZI7kLI3q8b89Khd74iQj29f2xq1UCrksKkpKzl0/edit

agenda snapshot:

  1.  Convene, take roll, review records and plan the next meeting(s).

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC, UTHSCSA (scribe), UTSW, MU, 
IndianaU, Utah, Allina, Intermountain

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): May 5; scribe: UTSW? MU?

*   Note scribe 
rotation
 appendix

  2.  Apr 2020 PCORnet CDM refresh: due Apr 27

 *   Done: 
UIOWA, 
UTHSCSA, 
Utah, 
MCRF, 
UNMC, 
Intermountain, 
UTSW , Allina, 
MCW

 *   At-risk?

  3.  
milestone:covid19wk
 3rd query due 27 Apr

 *   #759 
covid19 PCORNet 
datamarts

*   Debrief from COVID CDM Query #2 'fd1228_pmp_wp010_nsd3_v03_2020' - 
due Apr 20
Based on Expanded inclusion 
criteria (right?)

   *   MU - have to check, working on fixing Covid query, plan to 
respond today (21 Apr)

 *   CDM+ in May for COVID19? revised 
SOW Apr 20
Is attachment:COVID CDM+ 
SOW.docx​
 different, McClay? provenance?

*   RW to collect nominees for CDM+ workgroup. RC, ML

*   RW:  to ask how federated results will be made available (publicly)?

 *   #758 
covid19 ACT nodes refreshed 
2x/week

*   McClay “NCATS ACT is also proposing an i2b2 metadata build specific 
to COVID. I think this is relevant to ACT querying through SHRINE (COVID i2b2 
variables)”
Provenance of COVID i2b2 
VARIABLES.docx​?

  4.  
Milestone:tumor-reg-18

 *   #739 HERON 
NAACCR ETL outdated by v18
v0.3-electric-beta
 
cc28f83


wash your hands 
...


--
Dan

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gpc-dev 21 Apr agenda and meeing notes

[Dan Connolly]

What else for tomorrow?

UNMC is scheduled to scribe
https://docs.google.com/document/d/1IuLp9z_GWGGy2XnPsPhi6QzKsGZoPWwDIalPNWmdUUg/edit

agenda snapshot:


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC (scribe), UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Apr 28; scribe: UTSW? UTHSCSA?

*   Note scribe 
rotation
 appendix

  2.  Apr 2020 PCORnet CDM refresh: due Apr 27

 *   Done: 
UIOWA, 
UTHSCSA, 
Utah

 *   at-risk?

  3.  
milestone:covid19wk

 *   #759 
covid19 PCORNet 
datamarts

*   Debrief from COVID CDM Query #2 'fd1228_pmp_wp010_nsd3_v03_2020'
Based on Expanded inclusion 
criteria (right?)

   *   KUMC - done ~Apr 19

   *   UIOWA -

   *   MCW -

   *   MCRI -

   *   UNMC -

   *   UTHSCSA - weekly infeasible

   *   UTSW -

   *   MU -

   *   IndianaU - not planned

   *   Utah -

   *   Allina - done - expanded critieria 2x/week

   *   Intermountain -

 *   CDM+ in May for COVID19? revised 
SOW

 *   #758 
covid19 ACT nodes refreshed 
2x/week

*   KUMC working on DX mapping

*   KUMC working on [which?] new ontology

  4.  
Milestone:tumor-reg-18

 *   #739 HERON 
NAACCR ETL outdated by 
v18 - alpha


wash your hands 
...


--
Dan

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CDM+ in May for COVID19? revised SOW

[Dan Connolly]

Please estimate feasibility of tackling the attached revised state of work; for 
example, adding the elements in this table in the May time frame.


CDM+


Data element


Location in CDM (likely)


Inpatient vitals (respiratory rate, heart rate, O2 saturation, temperature)*


OBS_CLIN


Pulse oximetry/FiO2 ratio


OBS_CLIN


Admission to ICU


OBS_GEN or OBS_CLIN, depending on approach


Use of mechanical ventilation (beyond CPT code)


OBS_GEN or OBS_CLIN, depending on approach


Smoking status* (vaping status if available)


VITAL for smoking status; OBS_CLIN if vaping data available


Patient current address (especially zip – 5- or 9-digit)*


LDS_ADDRESS_HISTORY


Disposition* (already included in most datamarts)


ENCOUNTER


COVID-19 lab results (antigen & antibody)*


LAB_RESULT_CM


Chief complaint (Emergency Department)


CONDITION


Other labs relevant for COVID-19-related research*


LAB_RESULT_CM


*These data elements may already be available in the CDM for some datamarts; 
however, some items will need further investigation in order to define how best 
to represent them in the CDM.



We can discuss on the call tomorrow, but bonus points to anyone who replies in 
writing.



From: Russ Waitman 
Sent: Monday, April 20, 2020 8:47 AM
To: Dan Connolly 
Subject: COVID CDM revised SOW




COVID-19 Subset-CDM+_SOW.docx
Description: COVID-19 Subset-CDM+_SOW.docx
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Re: Date shifting for GROUSE

[Dan Connolly]

We don't require date shifting before you send your data; we just require that 
you tell us to what extent each patient's record has been shifted.

details are in...
#597 (spec for crosswalk to accompany i2b2 datamarts for 
GROUSE)

cited from tickets such as...
#732 (GROUSE Refresh 2019 - 
Iowa)

--
Dan


From: Gpc-dev  on behalf of Gryzlak, Brian M 

Sent: Friday, April 17, 2020 10:07 AM
To: gpc-dev@listserv.kumc.edu 
Subject: Date shifting for GROUSE


Hi,

Can someone confirm whether or not date shifting is or will be required for 
future data sent to KUMC for GROUSE?



My understanding was that it was not but need to confirm.



Thanks,

Brian



Brian M. Gryzlak, MSW, MA

Project Coordinator

S414 CPHB

319.335.8218

The University of Iowa

Iowa City, IA 52242

brian-gryz...@uiowa.edu



Health Effectiveness Research Center 
(HERCe)


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Re: De-id notes questions

[Dan Connolly]

a. yes, KUMC has an SOP for de-id clinical notes; we presented our adjudication 
process, a REDCap based regulatory review 
process
  at 
HackathonFour.
 The software we use to do the scrubbing is developed in collaboration with MCW:
https://bitbucket.org/MCW_BMI/notes-deidentification/src/master/
https://informatics.gpcnetwork.org/trac/Project/ticket/573#comment:18


b. yes, we make encounter, provider info available. I forget the rules for 
provider, but it's somewhere in our data request 
process,
 I'm pretty sure.

c. Yes, certain types of clinical notes are not made available; those that have 
not made it thru adjudication.

d. outside researchers... I'm not sure if that has happened, but I suppose our 
normal processes would accommodate it. The usual thing is to have a 
collaborator at KUMC.


From: Gpc-dev  on behalf of Gryzlak, Brian M 

Sent: Monday, April 13, 2020 3:59 PM
To: gpc-dev@listserv.kumc.edu 
Subject: De-id notes questions


Hi everyone,



A researcher at UIOWA is interested in knowing whether any GPC sites currently 
provide de-identified clinical notes to researchers.  The broad aim is to link 
clinical notes to other GPC data for a proposal on chemotherapy among 
overweight / obese patients with cancer to assess reasons for chemo dose 
variations.



Can sites please weigh in as to whether de-identified clinical notes are ever 
provided to researchers?



If so, answers to any/all of the following would be great to know:

  1.  Does your site use any standard processes to de-d clinical notes?  If so, 
can you please describe?
  2.  Are other attributes like provider, encounter info, etc. available along 
with the actual notes?
  3.  Are certain types of clinical notes not captured or not made available to 
researchers (e.g., phone consults that do not result in a provider referral, 
etc.)?
  4.  Have de-id notes ever been shared with outside researchers (i.e., 
researchers not currently affiliated with your site)?



Thanks!

Brian



Brian M. Gryzlak, MSW, MA

Project Coordinator

S414 CPHB

319.335.8218

The University of Iowa

Iowa City, IA 52242

brian-gryz...@uiowa.edu



Health Effectiveness Research Center 
(HERCe)


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gpc-dev 7 Apr agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

Allina is scheduled to scribe.
https://docs.google.com/document/d/179Zx9pA7eaqdKGHFj7jXtUsGR32DDWWQeSNK7gxOd8I/edit#

Agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: Allina

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   #757 (Carnahan ROA - Deprescribing and Outcomes in Older Adults 
with Delirium) created 
 Mar 13

 *   Next meeting(s): Apr 14; scribe: KUMC? UTSW?

*   Note scribe 
rotation
 appendix

  2.  Apr 2020 PCORnet CDM refresh: on track for Apr 15?
If you’re on track, add OK by your site. If you have something to discuss, add 
? for a question or ! to note a risk.

 *   KUMC OK; UIOWA; MCW; MCRI;  UNMC; UTHSCSA; UTSW; MU; IndianaU; Utah; 
Allina; Intermountain

  3.  
milestone:covid19wk

 *   #758 
covid19 ACT nodes refreshed 
2x/week

 *   #759 
covid19 PCORNet 
datamarts

*   standards relative to ICD, LOINC etc. to ensure we’re pulling the 
same thing out of our EHRs: JRC Updated ticket 
#759 with 4 slides 
and Excel spreadsheet of LOINC pre-release codes

*   Expanded inclusion 
criteria

 *   Chief complaint Jim will enquire for DRNOC if this can be included. 
(See also How to 
add…
 31 Mar)

 *   ‘Germwatch’ definition of COVID-19 positive. - Susan Rea to share the 
definition to list: Intermountain LOINC codes for COVID-19 tests 
   Susan Rea

  4.  
Milestone:tumor-reg-18

 *   Postponed to next (Apr? May?) KUMC HERON release.

 *   #739 HERON 
NAACCR ETL outdated by 
v18 - alpha / beta 
testing, some progress, available to test. Prebuilt jar files may not be up to 
date.

  5.  Trac user accounts: avall...@mcw.edu. DC to help.


wash your hands 
...

--
Dan

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gpc-dev Mar 31 agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

MCW is scheduled to scribe.
https://docs.google.com/document/d/1YUBJFrGgxGSyea9_XUi3e9NIAUSdT4cjxDNQl4OdHJ0/edit#

agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: MCW

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Apr 7; scribe: Allina? KUMC?

*   Note scribe 
rotation
 appendix

  2.  
milestone:covid19wk

 *   #759 
covid19 PCORNet datamarts
PCORnet Response to 
COVID-19
Russ will learn more in a meeting at noon March 24

 *   Maybe PCORNet would slip the deadline on the Apr refresh? Stephanie 
will inquire. Stand-by 
message Mar 25

 *   #758 
covid19 ACT nodes refreshed 
2x/week

 *   JRC: in covid cohort identification - Should Scott and I share data 
standards relative to ICD, LOINC etc. to ensure we’re pulling the same thing 
out of our EHRs? … JRC: I’ll send something to gpc-dev

  3.  i2b2 metadata for medications in the Nebraska Lexicon (#411)

  4.  
Milestone:tumor-reg-18

 *   #739 HERON 
NAACCR ETL outdated by 
v18 - alpha / beta 
testing

  5.  Trac user accounts: avall...@mcw.edu. DC to help.

--
Dan

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gpc-dev 24 Mar agenda and meeting notes

[Dan Connolly]

I added the COVID-19 item, but otherwise, I propose pretty much the same agenda 
as last week.

--
Dan



From: Dan Connolly
Sent: Monday, March 16, 2020 10:52 AM
To: gpc-dev@listserv.kumc.edu 
Subject: gpc-dev 17 Mar agenda and meeting notes

What else for tomorrow? I didn't find a lot, and none of it is urgent, so I 
welcome proposals to skip to next week.

Intermountain is scheduled to scribe. If we skip to next week, are you 
available? If not, Allina? MCW?
https://docs.google.com/document/d/1MgetN9WI-npQGDxqEytFmz8AUt2a7ICALnes2C4u62U/edit#


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 817-393-381; call +1 (571) 317-3131

 *   Roll; Reminder - put site after your name in GoToMeeting preferences
GPC DevTeams represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain

*   Today's scribe: Intermountain

 *   Comments on the agenda? (ref SoftwareDev#tracking) On last week’s 
notes? (#12)
Recent tickets opened/closed - FYI (i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Mar 24; scribe: Allina? MCW?

*   Note scribe rotation appendix

  2.  Datavant / PPRL

 *   Protocol is intended to be shared with local IRBs - link is broken, 
Brian to send to GPC Dev listserv: done Tue, Mar 10

  3.  Milestone:tumor-reg-18

 *   #739 HERON NAACCR ETL outdated by v18 - alpha / beta testing

p.s. Wash your hands and follow the rest of the CDC 
advice<https://www.cdc.gov/coronavirus/2019-ncov/prepare/prevention.html> to 
maintain good health.

--
Dan

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toward 2x/week refresh for COVID-19 cohort

[Dan Connolly]

A lot of discussion has been going around; here's hoping I find time to 
summarize. Meanwhile, everybody is welcome to chime in by email here and in 
tomorrow's call.

--
Dan

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Canceled: GPC Dev Weekly Teleconference

[Dan Connolly]

BEGIN:VCALENDAR
METHOD:CANCEL
PRODID:Microsoft Exchange Server 2010
VERSION:2.0
BEGIN:VTIMEZONE
TZID:Central Standard Time
BEGIN:STANDARD
DTSTART:16010101T02
TZOFFSETFROM:-0500
TZOFFSETTO:-0600
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END:STANDARD
BEGIN:DAYLIGHT
DTSTART:16010101T02
TZOFFSETFROM:-0600
TZOFFSETTO:-0500
RRULE:FREQ=YEARLY;INTERVAL=1;BYDAY=2SU;BYMONTH=3
END:DAYLIGHT
END:VTIMEZONE
BEGIN:VEVENT
ORGANIZER;CN=Dan Connolly:MAILTO:dconno...@kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=gpc-dev@li
 stserv.kumc.edu:MAILTO:gpc-dev@listserv.kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Geary, Car
 ol R":MAILTO:carolr.ge...@unmc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="McDowell, 
 Bradley D":MAILTO:bradley-mcdow...@uiowa.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Hillary Sa
 ndoval:MAILTO:hsando...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Imran Hafe
 ez:MAILTO:mhaf...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Tesch, Nat
 han K., M.S.":MAILTO:tesch.nat...@mayo.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Rodgers, C
 assandra R":MAILTO:cassandra.rodg...@allina.com
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Maren Lowr
 ance:MAILTO:mlowra...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Mandhadi, 
 Vasanthi (Medical Research Office)":MAILTO:mandha...@health.missouri.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Mazumder, 
 Narayana":MAILTO:narayana.mazum...@allina.com
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Mei Liu:MA
 ILTO:mei...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Moffett, E
 ric E":MAILTO:moffe...@uthscsa.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Gryzlak, B
 rian M":MAILTO:brian-gryz...@uiowa.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Mosa, Abu 
 S.":MAILTO:mo...@health.missouri.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Sanns, Wil
 liam":MAILTO:sa...@uthscsa.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Russ Waitm
 an:MAILTO:rwait...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=mrkfw:MAIL
 TO:mr...@health.missouri.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Brooklyn W
 inkel:MAILTO:bwink...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Osinski, K
 risten":MAILTO:kosin...@mcw.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Riley, Dan
 ielle":MAILTO:danielle-ri...@uiowa.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Tamara Win
 den:MAILTO:twin...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Kubacki-Me
 yer, Lynda M":MAILTO:kubacki-meyer.ly...@marshfieldresearch.org
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Campbell, 
 James R":MAILTO:campb...@unmc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Gassner,Co
 ry":MAILTO:cory.gass...@cerner.com
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gpc-dev 17 Mar agenda and meeting notes

[Dan Connolly]

What else for tomorrow? I didn't find a lot, and none of it is urgent, so I 
welcome proposals to skip to next week.

Intermountain is scheduled to scribe. If we skip to next week, are you 
available? If not, Allina? MCW?
https://docs.google.com/document/d/1MgetN9WI-npQGDxqEytFmz8AUt2a7ICALnes2C4u62U/edit#


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 817-393-381; call +1 (571) 317-3131

 *   Roll; Reminder - put site after your name in GoToMeeting preferences
GPC DevTeams represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain

*   Today's scribe: Intermountain

 *   Comments on the agenda? (ref SoftwareDev#tracking) On last week’s 
notes? (#12)
Recent tickets opened/closed - FYI (i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Mar 24; scribe: Allina? MCW?

*   Note scribe rotation appendix

  2.  Datavant / PPRL

 *   Protocol is intended to be shared with local IRBs - link is broken, 
Brian to send to GPC Dev listserv: done Tue, Mar 10

  3.  Milestone:tumor-reg-18

 *   #739 HERON NAACCR ETL outdated by v18 - alpha / beta testing

p.s. Wash your hands and follow the rest of the CDC 
advice to 
maintain good health.

--
Dan

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gpc-dev 10 Mar agenda and meeting notes

[Dan Connolly]

Please excuse the delay; I got caught up in NAACCR development 
(#739) yesterday.


Marshfield is scheduled to scribe
https://docs.google.com/document/d/1-PbVjnSZ7berUFkI6iUfWbX7rC_YBH9jH_MmjvrDOZA/edit

I'm just starting on the agenda...


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

  2.
  3.  stuff from last week 
(#12)
  4.  stuff from tickets by 
milestone
  5.  stuff from ​gpc-dev email
  6.  new/closed/reopened 
tickets


--
Dan

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gpc-dev 3 Mar agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UIowa is scheduled to scribe.
https://docs.google.com/document/d/1g688XbUyPledK84jEL9Ym0d9RVQ74dUmpqIv3QZOuPA/edit#

agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: UIowa

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   #15 (Install SNOMED scheme, map Diagnoses to SNOMED CT in KUH EMR) 
closed by  
wontfix

*   #16 (Install LOINC scheme, map Labs to LOINC in KUH EMR) closed 
 fixed

*   #304 (accuracy of ALS diagnosis data collection) closed 
 fixed

 *   Next meeting(s): Mar 10; scribe: Marshfield? Allina?

*   Note scribe 
rotation
 appendix

  2.  
Milestone:grouse-refresh-2

 *   All 12 sites submitted!

 *   #620 
annual update of GROUSE i2b2 data from sites
KUMC integration 
work scheduled for April

 *   #751 
GROUSE Refresh 2019 - 
Indiana - Submitted 
Feb 28; standing by for Song / Daryl to confirm receipt.

 *   #734 
GROUSE Refresh 2019 - 
Marshfield - KUMC 
to confirm some parts

  3.  #756 Allina 
i2b2 ACT SHRINE 
node - aim for May?

  4.  April PCORNet CDM refresh - status by site

--
Dan

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gpc-dev 25 Feb agenda and meeting notes

[Dan Connolly]

What else for our meeting today?

Utah is scheduled to scribe:
https://docs.google.com/document/d/1rCc1rOxWV21LrVuJE8LLxOSdA2Aq1t_H3MyfiF1HSjc/edit


agenda snapshot (please excuse the delay; I was home sick yesterday):


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: Utah

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Mar 3; scribe: Marshfield? UIowa?

*   Note scribe 
rotation
 appendix

  2.  
Milestone:grouse-refresh-2

 *   #755 (GROUSE Refresh 2019 - 
IHC) - done

 *   #731 
GROUSE Refresh 2019 - 
KUMC - done

 *   #751 
GROUSE Refresh 2019 - 
Indiana - Data is 
ready to go. Needing DBA support.

  3.  
Milestone:tumor-reg-18

 *   #739 HERON 
NAACCR ETL outdated by 
v18


--
Dan

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Re: Record Linkage/ Datavant work estimation

[Dan Connolly]

FYI, in the course of answering some questions as part of KUMC's security 
review, I started summarizing what I know about the PPRL project in a wiki page:

https://informatics.gpcnetwork.org/trac/Project/wiki/PPRL


From: Gpc-dev  on behalf of Mandhadi, 
Vasanthi (Medical Research Office) 
Sent: Tuesday, February 11, 2020 9:30 AM
To: gpc-dev@listserv.kumc.edu 
Subject: FW: Record Linkage/ Datavant work estimation


Hi All,



At MU, we are trying to estimate work effort needed for Datavant record linkage 
process and would like to know the following from other sites. Thank you.



  1.  How much work effort are other sites estimating for
 *   Initial installation of Datavant software
 *   Hash tokens creation and populating in CDM table



Dan, Can you please add this to today’s meeting agenda.





Thank you,

Vasanthi Mandhadi

Sr. Research Design Engineer

University of Missouri School of Medicine

(573) 882-6273


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18 Feb gpc-dev agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

IU is scheduled to scribe.
https://docs.google.com/document/d/1pMTfnbjVmLaydjsSxJJIwpBhi9-GTUqczpqZhwP0sos/edit


agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: IU

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Feb 25; scribe: Utah?, Marshfield?

*   Note scribe 
rotation
 appendix

  2.  Cycle 7 Refresh 2 EDC Reports
EDC reports: 
collection, publication

 *   11 of 12 received

 *   Intermountain will submit the report soon

  3.  agreements for including partner facility data
UTHSCSA to send data sharing MOU to UNMC

  4.  InCommon participation/testing 
   Thomas Van 
Doorn

  5.  
Milestone:next-d

 *   #713 NextD 
data refresh

*   Received by 23 Dec: UIOWA, MCW, IU, KUMC, UTSW, MU

*   MU - Marshall MU; Saw and am working on them, still..

*   Alona: We are asking each site how they map when a person goes to 
ED and ends up in IP.

   *   KUMC 4. one EI encounter

   *   UIOWA 4. one EI encounter

   *   IU

   *   MCW 3. one IP encounter

   *   UTSW 1. two encounters: one ED and one IP

   *   MU

   *   UNMC 4. one EI encounter

*   Alona: I’ll send something for MCW to look at.

*   Indiana: Quality issue pending.

  6.  #756 Allina 
i2b2 ACT SHRINE 
node created - 
upcoming meetings Feb 27, Mar 5

  7.  
Milestone:grouse-refresh-2

 *   #755 (GROUSE Refresh 2019 - IHC)
Crosswalk TODO - 
Susan / IHC to notify KUMC when ready

 *   #731 
GROUSE Refresh 2019 - 
KUMC -

 *   #751 
GROUSE Refresh 2019 - 
Indiana -

  8.  SSDMF 
DeathDataSharing

 *   DC to look into splitting the ~7GB datafile.
Done: brainstormed approaches; all non-trivial effort; asked Utah for detail; 
Utah said “have a work-around; don’t bother”

 *   SSDMF updates 
   Gryzlak, 
Brian M: “... how often SSDMF updates [...] are/can be sent to sites?”

*   "As part of each HERON release (ideally, monthly) KUMC staff get 
recent weekly updates from NTIS and prepare and distribute a table of hashed 
data." -- 
DeathDataSharing

--
Dan

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gpc-dev 11 Feb agenda and meeting notes

[Dan Connolly]

oops! I neglected to send this yesterday... What else for today's meeting?

MU is scheduled to scribe
https://docs.google.com/document/d/1mPEv7ScfeM8ElsxLSQf_BsqwsUUR3ycrOTTlJ_qHtUM/edit




  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: UTHSCSA

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Feb 18; scribe: IU?, Utah?

*   Note scribe 
rotation
 appendix

  2.  PCORNet CDM c7r2 refresh
EDC reports: collection, publication 
(http://www.gpcnetwork.org/?q=DataCharacterization)

 *   Sravani will be reaching out for that.
Cycle 7 Refresh 2 EDC Reports 
   Sravani 
Chandaka

  3.  
Milestone:next-d

 *   #713 NextD 
data refresh

*   Received by 23 Dec: UIOWA, MCW, IU, KUMC, UTSW, MU

*   MU - SES table - less than 5% of patients from Table 1 was geocoded

*   Alona: We are asking each site how they map when a person goes to 
ED and ends up in IP.

   *   KUMC 4. one EI encounter

   *   UIOWA 4. one EI encounter

   *   IU

   *   MCW 3. one IP encounter

   *   UTSW

   *   MU

   *   UNMC

*   Alona: KUMC please follow up with me and let me know where the file 
you uploaded on your site is. Dan C. I can do that

*   Marshal MU; Saw and am working on them.

*   Indiana: Jarrah- I will send you available dates and times. Need to 
get with the analyst that pulled the data.

  4.  
Milestone:grouse-refresh-2

 *   #755 (GROUSE Refresh 2019 - 
IHC) ETA  file 
transfer request sent Jan 31

 *   #731 
GROUSE Refresh 2019 - 
KUMC - ETA: Jan 31

 *   #751 
GROUSE Refresh 2019 - 
Indiana - ETA Feb 14

*   A few exported tables contained PHI and will need to be 
re-exported. Requests for export have been submitted as of 2/3/2020.

--
Dan

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Re: SSDMF updates

[Dan Connolly]

"As part of each HERON release (ideally, monthly) KUMC staff get recent weekly 
updates from NTIS and prepare and distributes a table of hashed data." -- 
https://informatics.gpcnetwork.org/trac/Project/wiki/DeathDataSharing



From: Gpc-dev  on behalf of Gryzlak, Brian M 

Sent: Friday, February 7, 2020 2:10 PM
To: gpc-dev@listserv.kumc.edu 
Subject: SSDMF updates


Hi,



Can KUMC please advise on how often SSDMF updates – like the one sent out 
yesterday - are/can be sent to sites?



Thanks,

Brian



Brian M. Gryzlak, MSW, MA

Project Coordinator

S414 CPHB

319.335.8218

The University of Iowa

Iowa City, IA 52242

brian-gryz...@uiowa.edu



Health Effectiveness Research Center 
(HERCe)


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gpc-dev 4 Feb agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UTHSCSA is scheduled to scribe
https://docs.google.com/document/d/1wzDdai4M45kusR_NTtLxlcNBn-Kz2FW5YZOh9IDwZz0/edit

agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: UTHSCSA

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Feb 11; scribe: IU? MU?

*   Note scribe 
rotation
 appendix

  2.  PCORNet CDM c7r2 refresh
due Jan 27. In case of delays, be sure to contact dr...@pcornet.org

 *   9 Approved: KUMC, UIOWA, MCW, MCRI, UNMC, Utah, Allina, UTSW, MU

 *   UTHSCSA - Technical difficulties. Hopefully submit in couple of days

 *   IndianaU - Error on Script. ETA Day or two

 *   Intermountain - Susan- Email to DRNOC about Sysdate variable

 *   EDC reports: collection, publication

  3.  ACT for non-CTSA sites (Allina, MCRF, MU)
i2b2 ad-hoc query using CDM datamarts (Allina, KUMC)

  4.  
Milestone:next-d

 *   #713 NextD 
data refresh

*   Received by 23 Dec: UIOWA, MCW, IU, KUMC, UTSW, MU

*   UNMC ETA for last table Jan 31

*   UTSW to re-send facility table with delimiters/facility_id after 
PCORI CDM Refresh.

*   KUMC: Mei - need to talk to xsong

*   MU - SES table - less than 5% of patients from Table 1 was geocoded

  5.  
Milestone:grouse-refresh-2

 *   #755 (GROUSE Refresh 2019 - 
IHC) ETA  Jan 31

 *   #731 
GROUSE Refresh 2019 - 
KUMC - ETA: Jan 31

 *   #754 (GROUSE Refresh 2019 - 
Utah) ETA Jan 31.

 *   #751 
GROUSE Refresh 2019 - 
Indiana - ETA Feb 4

  6.  GROUSE data purchase update


--
Dan

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Re: i2b2 on CDM, ACT integration

[Dan Connolly]

Yes, we'd like you to present / demo for a few minutes tomorrow during our 
weekly dev call. I expect if you just show us what you're up to and take a few 
questions, 10 or 20 minutes should suffice. I'm open to most any format that 
you prefer.

I'm not aware yet of any motivation for a separate session, but we can see how 
it goes.

From: Mazumder, Narayana 
Sent: Monday, February 3, 2020 9:20 AM
To: Dan Connolly ; gpc-dev@listserv.kumc.edu 

Cc: Nathan Hensel ; Raj, Vino S ; 
Rodgers, Cassandra R 
Subject: RE: i2b2 on CDM, ACT integration


Hi Dan,



We will be happy to present our implementation of i2b2 on CDM. Would you like 
us to present it during our weekly DEV call? We are also open to having a 
separate session where we can brainstorm ACT integration, best practices and 
other enhancements.



Thank you

Narayana



From: Dan Connolly 
Sent: Monday, February 3, 2020 9:10 AM
To: gpc-dev@listserv.kumc.edu
Cc: Nathan Hensel ; Mazumder, Narayana 

Subject: i2b2 on CDM, ACT integration



Russ and company had a conversation about non-CTSA hubs joining ACT. We've 
heard Narayana at Allina is working on i2b2 on CDM. Nathan here at KUMC is 
doing related work. We'd like to have a show and tell of progress in that area 
and brainstorm about integrating it with the ACT network.



--

Dan Connolly



[http://www.allinahealth.org/uploadedImages/Content/ah-header-logo.png]<http://protect-us.mimecast.com/s/C7WoCER26mhpzxYKINKYm3?domain=allinahealth.org>
This message contains information that is confidential and may be privileged. 
Unless you are the addressee (or authorized to receive for the addressee), you 
may not use, copy or disclose to anyone the message or any information 
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i2b2 on CDM, ACT integration

[Dan Connolly]

Russ and company had a conversation about non-CTSA hubs joining ACT. We've 
heard Narayana at Allina is working on i2b2 on CDM. Nathan here at KUMC is 
doing related work. We'd like to have a show and tell of progress in that area 
and brainstorm about integrating it with the ACT network.

--
Dan Connolly

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gpc-dev 28 Jan agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UNMC is scheduled to scribe.
https://docs.google.com/document/d/1Pw4UCDfVLyMG0ADnYSmvo_j96beCfmnNcDNWiPM8_YQ/edit

agenda snapshot:


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: UNMC

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Feb 4; scribe: UTHSCSA? IU?

*   Note scribe 
rotation
 appendix

*   i2b2/CDM

*   ACT for non-CTSA sites (Allina, MCRF, MU)

  2.  PCORNet CDM c7r2 refresh
due Jan 27. In case of delays, be sure to contact dr...@pcornet.org

 *   7 Approved: KUMC, UIOWA, MCW, MCRI, UNMC, Utah, Allina

 *   UTHSCSA -

 *   UTSW -

 *   MU -

 *   IndianaU -

 *   Intermountain -

  3.  
Milestone:next-d
 due Dec 18

 *   #713 NextD 
data refresh

*   Received by 23 Dec: UIOWA, MCW, IU, KUMC, UTSW, MU

*   UNMC ETA for last table Jan 31

*   UTSW to re-send facility table with delimiters/facility_id after 
PCORI CDM Refresh.

*   KUMC: Mei to propose time to meet/discuss with Alona

*   MU - SES table - less than 5% of patients from Table 1 was geocoded

  4.  
Milestone:grouse-refresh-2

 *   #755 (GROUSE Refresh 2019 - 
IHC) ETA  Jan 31

 *   #731 
GROUSE Refresh 2019 - 
KUMC - ETA: Jan 31

 *   #754 (GROUSE Refresh 2019 - 
Utah) ETA Jan 31.

 *   #751 
GROUSE Refresh 2019 - 
Indiana - ETA for 
CDM, i2b2 corresponding to finder file: Feb 4

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gpc-dev 21 Jan agenda and meeting notes

[Dan Connolly]

What else for today's meeting?

UTSW is scheduled to scribe
https://docs.google.com/document/d/1GnzV370VxbLvDF4_F4Ej9NTU-kjwOQmoEwEIlQ1q2xU/edit#

agenda snapshot (please excuse the delay; yesterday was a KUMC holiday to honor 
Dr. Martin Luther King):


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: UTSW

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 (#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   #17 (provider identification across sites) closed 
 fixed

*   #65 (handle hosts other than localhost in dblink_deid_id) closed 
 fixed

*   #77 (GPC shared SNOMED terms for clinical findings, history, 
organisms) closed 
 
superseded

*   #50 (support db_domain in HERON ETL database connections) closed 
 fixed

*   #25 (make MU2 version of snomed available to gpc-dev) closed 
 wontfix

*   #601 (Advice on Oracle/SQL Server maintenance protocols) 
closed 
wontfix

*   #53 (V1.7 patient_mapping table has project_id as part of primary 
key and the ...) 
closed 
wontfix

 *   Next meeting(s): Jan 21; scribe: UNMC? UTHSCSA?

*   Note scribe 
rotation
 appendix

  2.  
Milestone:next-d
 due Dec 18

 *   #713 NextD 
data refresh

*   Received by 23 Dec: UIOWA, MCW, IU, KUMC, UTSW, MU

*   UNMC ETA for last table (socioeconomic status) Jan 17

*   UTSW to re-send facility table with delimiters

*   Encounters not linked to FACILITYID

   *   KUMC: Mei to propose time to meet/discuss with Alona

   *   UIOWA: BG to follow up on whether these AV encounters can be 
filled in with facility info.

   *   UTSW / Philip to look into why facility_id is not populated.

  3.  CDM refresh comes out Jan 6; due Jan 27

 *   Approved: Allina (Jan 19)

 *   UIOWA: planning to submit Jan 14

 *   … Experience reports? Issues? Risks?

  4.  
Milestone:grouse-refresh-2

 *   #751 
GROUSE Refresh 2019 - 
Indiana - ETA for 
CDM, i2b2 corresponding to finder file: 21 Jan

 *   #755 (GROUSE Refresh 2019 - 
IHC) ETA  Jan 31

 *   #731 
GROUSE Refresh 2019 - 
KUMC - ETA: Jan 31

 *   #754 (GROUSE Refresh 2019 - 
Utah) ETA Jan 31.


--
Dan

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gpc-dev 14 Jan agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

KUMC is scheduled to scribe
https://docs.google.com/document/d/1pcfwNwRdOsHUq5KHBtnaQqffD6Gn2RdTzUNJuzimAvI/edit#

agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: KUMC

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Jan 21; scribe: UTSW? UNMC?

*   Note scribe 
rotation
 appendix

  2.  
Milestone:next-d
 due Dec 18

 *   #713 NextD 
data refresh

*   Received by 23 Dec: UIOWA, MCW, IU, KUMC, UTSW, MU

*   UNMC - ETA Jan 10

  3.  CDM refresh comes out Jan 6; due Jan 27
Experience reports? Issues? Risks?

  4.  
Milestone:grouse-refresh-2

 *   #751 
GROUSE Refresh 2019 - 
Indiana - ETA Jan 7

 *   #755 (GROUSE Refresh 2019 - 
IHC) ETA  Jan 21.

 *   #731 
GROUSE Refresh 2019 - 
KUMC - ETA: Jan 31

 *   #754 (GROUSE Refresh 2019 - 
Utah) ETA Jan 31.

--
Dan

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gpc-dev 7 Jan agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

Intermountain is scheduled to scribe
https://docs.google.com/document/d/1oLHW-TbXAAEZrPVX1c6cAzw_9fc-zwJY0sudZqUWcoU/edit#

agenda snapshot:


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences 
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: Intermountain

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Jan 14; scribe: KUMC? UTSW?

*   Note scribe 
rotation
 appendix

  2.  
Milestone:next-d
 due Dec 18

 *   #713 NextD 
data refresh

*   Received by 23 Dec: UIOWA, MCW, IU, KUMC, UTSW, MU

*   UNMC?

  3.  CDM refresh comes out Jan 6; due ~Jan 27

 *   Experience reports? Issues? risks?

  4.  
Milestone:grouse-refresh-2

 *   #731 
GROUSE Refresh 2019 - 
KUMC - ETA: Dec 20

 *   #734 (GROUSE Refresh 2019 - 
Marshfield)
 reopened Nov 29
owner: dbudine @ KUMC

 *   #751 
GROUSE Refresh 2019 - 
Indiana - ETA Jan 7

 *   #754 (GROUSE Refresh 2019 - Utah) 
created requested 
by Jan 30
Note questions from 
Reid

 *   #755 (GROUSE Refresh 2019 - IHC) 
created

  5.  #688 SSDMF / 
DeathDataSharing
 All GPC sites have access to the national death database

 *   BG: “can KUMC please advise on what basis sites can incorporate SSDMF 
data into their local data holdings”
RW repiled Fri 12/20/2019 2:48 PM; does that suffice?

--
Dan

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gpc-dev 17 Dec agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

MCW is scheduled to scribe.
https://docs.google.com/document/d/185CYDURwRRYPMhe32zXn1YgaCUKWyMmFDtxXKlyew60/edit#

agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences 
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: MCW

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Jan 7; scribe: Intermountain

*   Note scribe 
rotation
 appendix

*   CDM refresh comes out Jan 6; due ~Jan 27

  2.  GPC DROC Feasibility Request 
#57 Dr. Chetan 
P. Hans from Mizzou

 *   Data received from Intermountain, MCW, Marshfield, Utah, Missouri, 
Allina, Indiana

 *   KUMC - (10 Dec): query hanging; working with MU folks

  3.  
Milestone:next-d
 due Dec 18

 *   #713 NextD 
data refresh - 
UIOWA, UNMC, MCW, IU, KUMC, UTSW, MU

  4.  
Milestone:grouse-refresh-2

 *   #733 
GROUSE Refresh 2019 - 
UNMC - submitted 
Dec 10

 *   #731 
GROUSE Refresh 2019 - 
KUMC - ETA: Dec 20

 *   #734 (GROUSE Refresh 2019 - 
Marshfield)
 reopened Nov 29
owner: dbudine @ KUMC

 *   #751 
GROUSE Refresh 2019 - 
Indiana - ETA ~Dec 
3 (staff turnover)

 *   #740 GPC 
feasibity queries using datamarts submitted for GROUSE
Nathan @ KUMC has 
just started work on using CDM as an i2b2 datamart.

  5.  #688 SSDMF / 
DeathDataSharing
 All GPC sites have access to the national death database

 *   Last update(s): Nov 12, …
UIowa doesn’t see the Nov update. DC to check. DC sent encryption / hash keys 
Dec 11.

 *   BG: “can KUMC please advise on what basis sites can incorporate SSDMF 
data into their local data holdings (e.g., research data warehouses) aside from 
/ in addition to informing deceased patients in the CDM proper (e.g., is there 
a license agreement, is this part of the GPC DSA, etc?)? UIOWA would like to 
use the SSDMF to flag deceased patients in our research warehouse generally, 
such that patients who are deceased will also be flagged in the CDM. Before we 
take this step we want to be sure we have permission.”

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Re: GPC DROC Feasibility Request #57

[Dan Connolly]

Does this merit discussion in tomorrow's gpc-dev meeting? Sravani, is KUMC done?

From: Dan Connolly 
Sent: Monday, December 9, 2019 12:39 PM
To: Maren Lowrance ; 'gpc-d...@listserv.kumc.edu' 
; gpc-dev@listserv.kumc.edu 

Cc: han...@health.missouri.edu ; Sravani Chandaka 

Subject: Re: GPC DROC Feasibility Request #57

Sravani has been in touch with MU folks about technical issues.

Jarrah, what news since "Will update group with new ETA status later today Dec 
3"?

From: Gpc-dev  on behalf of Maren Lowrance 

Sent: Wednesday, November 13, 2019 11:16 AM
To: 'gpc-d...@listserv.kumc.edu' ; 
gpc-dev@listserv.kumc.edu 
Cc: han...@health.missouri.edu 
Subject: GPC DROC Feasibility Request #57


Good afternoon,



The SAS code for GPC DROC Feasibility Request 
#57<https://redcap.gpcnetwork.org/redcap_v6.11.5/DataEntry/index.php?pid=16=gpc_droc_oversight_request=57_id=53>
 has been uploaded to the request. Once your site has approved the DROC 
request, please run the query and submit counts via this REDCap 
survey.<https://redcap.gpcnetwork.org/surveys/?s=H9TWYYYK7R>



Please let me know if you have any questions!



Thank you,



Maren Lowrance

Greater Plains Collaborative Honest Broker

Clinical Informatics Coordinator

913-588-7688




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Re: gpc-dev 10 agenda and meeting notes

[Dan Connolly]

Sigh. The bad guys have made it so difficult that the KUMC enterprise defences 
decided to encrypt the PDF copy of our meeting notes.

https://docs.google.com/document/d/1aaWD6XFKNkMyG8YO3mjqG6b3tdBT5Zr42Q8D66SBtMU/edit

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Canceled: GPC Dev Weekly Teleconference

[Dan Connolly]

BEGIN:VCALENDAR
METHOD:CANCEL
PRODID:Microsoft Exchange Server 2010
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BEGIN:STANDARD
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BEGIN:VEVENT
ORGANIZER;CN=Dan Connolly:MAILTO:dconno...@kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=gpc-dev@li
 stserv.kumc.edu:MAILTO:gpc-dev@listserv.kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Geary, Car
 ol R":MAILTO:carolr.ge...@unmc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="McDowell, 
 Bradley D":MAILTO:bradley-mcdow...@uiowa.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Hillary Sa
 ndoval:MAILTO:hsando...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Imran Hafe
 ez:MAILTO:mhaf...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Tesch, Nat
 han K., M.S.":MAILTO:tesch.nat...@mayo.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Rodgers, C
 assandra R":MAILTO:cassandra.rodg...@allina.com
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Maren Lowr
 ance:MAILTO:mlowra...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Mandhadi, 
 Vasanthi (Medical Research Office)":MAILTO:mandha...@health.missouri.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Mazumder, 
 Narayana":MAILTO:narayana.mazum...@allina.com
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Mei Liu:MA
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Sanns, Wil
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Russ Waitm
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=mrkfw:MAIL
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Brooklyn W
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Osinski, K
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Riley, Dan
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Tamara Win
 den:MAILTO:twin...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Kubacki-Me
 yer, Lynda M":MAILTO:kubacki-meyer.ly...@marshfieldresearch.org
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Campbell, 
 James R":MAILTO:campb...@unmc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Wilkinson,
  Katie":MAILTO:wilkinso...@health.missouri.edu
DESCRIPTION;LANGUAGE=en-US:\n
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 01000444ABC592BDF7A449C058C7DCB8A15DC
RECURRENCE-ID;TZID=Central Standard Time:20191231T11
SUMMARY;LANGUAGE=en-US:Canceled: GPC Dev Weekly Teleconference
DTSTART;TZID=Central Standard Time:20191231T11
DTEND;TZID=Central Standard Time:20191231T12
CLASS:PUBLIC
PRIORITY:1
DTSTAMP:20191211T171044Z
TRANSP:TRANSPARENT
STATUS:CANCELLED
SEQUENCE:3
LOCATION;LANGUAGE=en-US:https://global.gotomeeting.com/meeting/join/8173933
 81
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END:VEVENT
END:VCALENDAR
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Canceled: GPC Dev Weekly Teleconference

[Dan Connolly]

BEGIN:VCALENDAR
METHOD:CANCEL
PRODID:Microsoft Exchange Server 2010
VERSION:2.0
BEGIN:VTIMEZONE
TZID:Central Standard Time
BEGIN:STANDARD
DTSTART:16010101T02
TZOFFSETFROM:-0500
TZOFFSETTO:-0600
RRULE:FREQ=YEARLY;INTERVAL=1;BYDAY=1SU;BYMONTH=11
END:STANDARD
BEGIN:DAYLIGHT
DTSTART:16010101T02
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TZOFFSETTO:-0500
RRULE:FREQ=YEARLY;INTERVAL=1;BYDAY=2SU;BYMONTH=3
END:DAYLIGHT
END:VTIMEZONE
BEGIN:VEVENT
ORGANIZER;CN=Dan Connolly:MAILTO:dconno...@kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=gpc-dev@li
 stserv.kumc.edu:MAILTO:gpc-dev@listserv.kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Geary, Car
 ol R":MAILTO:carolr.ge...@unmc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="McDowell, 
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Hillary Sa
 ndoval:MAILTO:hsando...@kumc.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Imran Hafe
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Tesch, Nat
 han K., M.S.":MAILTO:tesch.nat...@mayo.edu
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Rodgers, C
 assandra R":MAILTO:cassandra.rodg...@allina.com
ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Maren Lowr
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Mandhadi, 
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Moffett, E
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Riley, Dan
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN=Tamara Win
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Kubacki-Me
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DTSTART;TZID=Central Standard Time:20191224T11
DTEND;TZID=Central Standard Time:20191224T12
CLASS:PUBLIC
PRIORITY:1
DTSTAMP:20191211T171030Z
TRANSP:TRANSPARENT
STATUS:CANCELLED
SEQUENCE:2
LOCATION;LANGUAGE=en-US:https://global.gotomeeting.com/meeting/join/8173933
 81
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X-MICROSOFT-DISALLOW-COUNTER:FALSE
END:VEVENT
END:VCALENDAR
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gpc-dev 10 agenda and meeting notes

[Dan Connolly]

Anything else for tomorrow? My usual scan didn't turn up much.


  1.  Convene, take roll, review records and plan next meeting(s)
11:00 a.m. Central Time.
Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

Allina is scheduled to scribe
https://docs.google.com/document/d/1aaWD6XFKNkMyG8YO3mjqG6b3tdBT5Zr42Q8D66SBtMU/edit

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Re: GPC DROC Feasibility Request #57

[Dan Connolly]

Sravani has been in touch with MU folks about technical issues.

Jarrah, what news since "Will update group with new ETA status later today Dec 
3"?

From: Gpc-dev  on behalf of Maren Lowrance 

Sent: Wednesday, November 13, 2019 11:16 AM
To: 'gpc-d...@listserv.kumc.edu' ; 
gpc-dev@listserv.kumc.edu 
Cc: han...@health.missouri.edu 
Subject: GPC DROC Feasibility Request #57


Good afternoon,



The SAS code for GPC DROC Feasibility Request 
#57
 has been uploaded to the request. Once your site has approved the DROC 
request, please run the query and submit counts via this REDCap 
survey.



Please let me know if you have any questions!



Thank you,



Maren Lowrance

Greater Plains Collaborative Honest Broker

Clinical Informatics Coordinator

913-588-7688




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gpc-dev 3 Dec agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UIowa is scheduled to scribe.
https://docs.google.com/document/d/1OrEVmW6YfzbwK5sIU3ugue6_hJSq5KQVyQCm9s4ZZnI/edit


agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences 
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: Iowa

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Dec. 10rd scribe Allina? MCW?

*   Note scribe 
rotation
 appendix

  2.  
Milestone:grouse-refresh-2

 *   Ticket #727 (Finder file for Allina, Utah, IHC) 
reopened:
 “Utah need to resend finder file with patient_num_hash to GDIT”
ETA: send by Fri Nov 29.

*   Still in progress. Get back to it Monday, 12/2 after vacations

 *   #751 
GROUSE Refresh 2019 - 
Indiana - ETA ~Dec 3

 *   #733 
GROUSE Refresh 2019 - 
UNMC - ETA Dec 6

 *   #731 
GROUSE Refresh 2019 - 
KUMC - ETA: Dec 20

  3.  GPC DROC Feasibility Request #57
Dr. Chetan P. 
Hans from Mizzou

 *   Data received from Intermountain, MCW, Marshfield, Utah, Missouri, 
Allina

 *   Need data to be submitted on the Request #57 Result 
Submission from the 
following sites:

*   Indiana: - ETA 30 Nov

*   KUMC - ETA 30 Nov

  4.  
Miletstone:next-d
 due 2019-12-18

 *   #713 NextD 
data refresh

*   MCW is requested to contact AF in order to discuss format 
convenient for reporting insurance information.

*   All sites (KUMC, UIowa, MCW, UNMC, UTSW, IU, MU): data requested by 
2019-12-18

  5.  CDM C7R1 due Monday, October 28th

 *   11 Approved: KUMC, MCW, MCRI, UNMC, UTHSCSA, MU, Utah, Allina, 
Intermountain, UIOWA (25 Oct, Nov 5), UTSW (Nov 6)

 *   IndianaU: Submitted 11/26.

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gpc-dev 26 Nov agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

Marshfield is scheduled to scribe
https://docs.google.com/document/d/150DTZLyEDR-PljEBUxnduCd3ljUNhjt0Jv76dopw12I/edit

agenda snapshot:


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences 
GPC DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: Marshfield

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s): Dec. 3rd scribe scribe: Iowa

*   Note scribe 
rotation
 appendix

  2.  CDM C7R1 due Monday, October 28th

 *   11 Approved: KUMC, MCW, MCRI, UNMC, UTHSCSA, MU, Utah, Allina, 
Intermountain, UIOWA (25 Oct, Nov 5), UTSW (Nov 6)

 *   IndianaU: target completion date is 11/22

  3.  
Milestone:grouse-refresh-2

 *   Ticket #727 (Finder file for Allina, Utah, IHC) 
reopened:
 “Utah need to resend finder file with patient_num_hash to GDIT”
ETA: send by Fri Nov 29.

 *   #731 
GROUSE Refresh 2019 - 
KUMC - juggling…

 *   #733 
GROUSE Refresh 2019 - 
UNMC - ETA 
“beginning of November”

 *   #751 
GROUSE Refresh 2019 - 
Indiana - ETA ~Dec 3

  4.  GPC DROC Feasibility Request 
#57   Maren 
Lowrance
Note updated SAS code available via REDCap

 *   Dr. Chetan P. Hans from Mizzou

 *   Need data to be submitted on the Request #57 Result 
Submission from the 
following sites:

*   Indiana: - by the end of November.

*   Intermountain - needs access to query, find it in Redcap, Reid 
(UTAH) sending SAS query 19 Nov.

*   KUMC - ETA end of November.

*   MCW - submitted

*   Marshfield - submitted

*   Utah -

*   Missouri - submitted



--
Dan

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gpc-dev 19 Nov agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

Utah is scheduled to scribe
https://docs.google.com/document/d/1wa4QmQl8PE1zhcboUH7B25afgoRoMNVahr_L2Bv_cKE/edit#


agenda snapshot:


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in 
GoToMeeting preferences

*   GPC 
DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: Utah

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   None this week

 *   Next meeting(s)/scribe: Nov 25 Scribe: Marshfield? Iowa?

*   Note scribe 
rotation
 appendix

  2.  CDM C7R1 due Monday, October 28th

 *   11 Approved: KUMC, MCW, MCRI, UNMC, UTHSCSA, MU, Utah, Allina, 
Intermountain, UIOWA (25 Oct, Nov 5), UTSW (Nov 6)

 *   IndianaU: target completion date is 11/15.

  3.  Adaptable: how to send death 
data?  Vasanthi 
Mandhadi

 *   Brian: will contact Daneille and send info to 
gpc-dev@listserv.kumc.edu on how to get it and send it; in case email 
discussion doesn’t suffice, invite her to next week’s gpc-dev call.
In progress: Nov 12 
message

  4.  GPC DROC Feasibility Request 
#57   Maren 
Lowrance
Note updated SAS code available via REDCap

  5.  
Milestone:grouse-refresh-2

 *   Ticket #727 (Finder file for Allina, Utah, IHC) 
reopened:
 “Utah need to resend finder file with patient_num_hash to GDIT”

  6.  
Milestone:next-d
 due Dec 13
#713 NextD data 
refresh

 *   KUMC:

*   submitted IRB change request Nov 4

*   on track for data delivery by Dec 13

 *   UIOWA:

*   submitted IRB change request Nov 15.

*   Dec 13 data delivery feasible?

 *   MU: Abu Mosa

 *   MCW: Kris Osinski

 *   UNMC: Jim McClay

 *   UTSW: Phillip Reeder

 *   IU: Jarrah Hamer


--
Dan

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Re: Adaptable: how to send death data? [was: gpc-dev weekly...]

[Dan Connolly]

Brian, I did some post-meeting editing of the notes on this discussion:


  1.  Adaptable: how to send death 
data?<http://listserv.kumc.edu/pipermail/gpc-dev/2019q4/005406.html>  Vasanthi 
Mandhadi

 *   DC polls a few sites and discovers this whole issue / request is news 
to several sites.
Mosa/MU: It originates from an Oct 10 2019 GPC adaptable meeting. There’s an 
action item: All sites provide date of death for patients, once per week. By 
email.

 *   Stefani/Marshfield: any particular format?
Vasanthi/MU: golden ticket number and death date
Note MCW’s 
approach<http://listserv.kumc.edu/pipermail/gpc-dev/2019q4/005408.html>

 *   Mosa: email seems like an odd mechanism; I’d rather they used a 
process based on the portal.

 *   DC: is this consistent with established governance?
Russ: not sure; Defer to Danielle.
Brian: Danielle is the ADAPTABLE coordinator for GPC; she’s at UIOWA, where the 
IRB of record sits.
Vasanthi: I already checked with her.
Susan/Intermountain: our IRB calls golden ticket limited data, since attached 
to a person. [not to mention date of death is limited data]

 *   DC: Sounds like Vasanthi already checked with Danielle…
Various people are still interested in clarification / confirmation.
Brian: will contact Daneille and send info to gpc-dev@listserv.kumc.edu on how 
to get it and send it; in case email discussion doesn’t suffice, invite her to 
next week’s gpc-dev call.

https://docs.google.com/document/d/1EDUyksQTDa7ZK96nCpIYUX6eU6j1O9dWvJ_nKNoRJb4/edit

________
From: Dan Connolly 
Sent: Tuesday, November 12, 2019 9:25 AM
To: Mandhadi, Vasanthi (Medical Research Office) 
Cc: gpc-dev@listserv.kumc.edu 
Subject: Adaptable: how to send death data? [was: gpc-dev weekly...]




From: Mandhadi, Vasanthi (Medical Research Office) 

Sent: Monday, November 11, 2019 1:02 PM
To: Dan Connolly 
Subject: Re: gpc-dev weekly: scribe for Nov 12? cancel Nov 5

Hi Dan,

Can you please add this to tomorrow’s agenda (Nov 12).

Adaptable team requested to send death data to DCRI either once a week or once 
every 2 weeks. How are other sites sending this data?


Thank you,
Vasanthi Mandhadi

On Nov 4, 2019, at 9:39 AM, Dan Connolly 
mailto:dconno...@kumc.edu>> wrote:

MU, are you available to scribe next week? (Nov 12). In case they're not, how 
about you, Utah?

I don't see enough business to merit a meeting tomorrow, so let's cancel.

Congrats on getting CDM C7R1 approved, KUMC, MCW, MCRI, UNMC, UTHSCSA, MU, 
Utah, Allina, Intermountain.

--
Dan

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Re: gpc-dev weekly: scribe for Nov 12? cancel Nov 5

[Dan Connolly]

Thanks, Todd.

Agenda in progress:
https://docs.google.com/document/d/1EDUyksQTDa7ZK96nCpIYUX6eU6j1O9dWvJ_nKNoRJb4/edit

11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381<https://global.gotomeeting.com/meeting/join/817393381>; call +1 
(571) 317-3131

From: McNeeley, Todd Alexander 
Sent: Monday, November 4, 2019 9:41 AM
To: Dan Connolly ; gpc-dev@listserv.kumc.edu 

Subject: RE: gpc-dev weekly: scribe for Nov 12? cancel Nov 5


MU can scribe on the Nov. 12th.



From: Gpc-dev  On Behalf Of Dan Connolly
Sent: Monday, November 4, 2019 9:39 AM
To: gpc-dev@listserv.kumc.edu
Subject: gpc-dev weekly: scribe for Nov 12? cancel Nov 5



MU, are you available to scribe next week? (Nov 12). In case they're not, how 
about you, Utah?



I don't see enough business to merit a meeting tomorrow, so let's cancel.



Congrats on getting CDM C7R1 approved, KUMC, MCW, MCRI, UNMC, UTHSCSA, MU, 
Utah, Allina, Intermountain.



--

Dan


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Adaptable: how to send death data? [was: gpc-dev weekly...]

[Dan Connolly]

From: Mandhadi, Vasanthi (Medical Research Office) 

Sent: Monday, November 11, 2019 1:02 PM
To: Dan Connolly 
Subject: Re: gpc-dev weekly: scribe for Nov 12? cancel Nov 5

Hi Dan,

Can you please add this to tomorrow’s agenda (Nov 12).

Adaptable team requested to send death data to DCRI either once a week or once 
every 2 weeks. How are other sites sending this data?


Thank you,
Vasanthi Mandhadi

On Nov 4, 2019, at 9:39 AM, Dan Connolly 
mailto:dconno...@kumc.edu>> wrote:

MU, are you available to scribe next week? (Nov 12). In case they're not, how 
about you, Utah?

I don't see enough business to merit a meeting tomorrow, so let's cancel.

Congrats on getting CDM C7R1 approved, KUMC, MCW, MCRI, UNMC, UTHSCSA, MU, 
Utah, Allina, Intermountain.

--
Dan

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Canceled: GPC Dev Weekly Teleconference

[Dan Connolly]

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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Tesch, Nat
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Rodgers, C
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ATTENDEE;ROLE=OPT-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=TRUE;CN="Mandhadi, 
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gpc-dev weekly: scribe for Nov 12? cancel Nov 5

[Dan Connolly]

MU, are you available to scribe next week? (Nov 12). In case they're not, how 
about you, Utah?

I don't see enough business to merit a meeting tomorrow, so let's cancel.

Congrats on getting CDM C7R1 approved, KUMC, MCW, MCRI, UNMC, UTHSCSA, MU, 
Utah, Allina, Intermountain.

--
Dan

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CDM C7R1 status at UIOWA, UTSW, IU?

[Dan Connolly]

Brian, Phillip, Jarrah, what's the current status at your site?


 *UIOWA: 
Approved 25 Oct, 
but will need to re-submit with values of FACILITY_ID populated for the BP 
Track study.

 *   UTSW: (29 Oct): having challenges connecting to database. Is actively 
working on resolving the issue and will submit as soon as it’s resolved

 *   IndianaU: Target completion date: 11/4

--
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gpc-dev 22 Oct agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UTHSCSA is scheduled to scribe
https://docs.google.com/document/d/1fPoDn0pdVvC-Mct58X7wkGD2rNiId8aNZ9JG_WCbcf4/edit

agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in GoToMeeting preferences

*   GPC 
DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: UTHSCSA

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   DC to follow up re MU Security Death Master file (SSDMF) 
distribution / hashing

*   
HackathonSeven
 notes are as done as they’re likely to get

 *   Next meeting(s)/scribe: Oct 29? Nov 5? Scribe? IU? MU?

*   DC out Oct 29

*   Note scribe 
rotation
 appendix

  2.  CDM c7r1 due Monday, October 28th
FW: Data Curation Cycle 7 
updates   Roush, 
Steffani

 *   Status by site

*   KUMC:

*   UIOWA:

*   MCW:

*   MCRI: approved Oct 17

*   UNMC:

*   UTHSCSA - 10-14-2019 - APPROVED (?)

*   UTSW:

*   MU:

*   IndianaU:

*   Utah: approved Oct 21

*   Allina:

*   Intermountain:

  3.  GPC DROC Request 
#55,
 due 10/25

  4.  Babel/ DROC 55 
question   
Gryzlak, Brian M
“A demo on Tuesday would be helpful ...”


--
Dan

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Re: Babel/ DROC 55 question

[Dan Connolly]

Do you have 
PortQuery 
installed? The "XML Message Stack" stuff is a little obscure. I can demo on 
Tuesday.
PortQuery user directions

  1.  In the other i2b2 (i.e. babel):
 *   Run a query.
*   Make sure debug mode is on: look for the Show XML Message Stack 
button: <>, especially in the top right Query Tool section.
 *   Open the XML Message Stack and find the 
runQueryInstance_fromQueryDefinition message for your query (recent messages 
are at the bottom of the list)
 *   Copy the query_definition element, including its tags.
  2.  Then, in this i2b2,
 *   Paste below.
 *   Hit Load Query below.
 *   Select the Find Patients tab to see your query.

Installation

Installation follows the i2b2 plug-in 
install/register
 model.

The deploy/add_to_site.py script can help:

$ webclient=...htdocs/i2b2/webclient
$ plugins=${webclient}/js-i2b2/cells/plugins
$ mkdir -p ${plugins}/HERON
$ unzip -q -o -d ${plugins}/HERON/PortQuery/ portaquery.zip
$ python ${plugins}/WIP/PortQuery/deploy/add_to_cell.py PortQuery 
${webclient}/js-i2b2/i2b2_loader

https://bitbucket.org/DanC/portaquery/src/default/ <- 
https://informatics.gpcnetwork.org/trac/Project/wiki/PortQuery



From: Gpc-dev  on behalf of Gryzlak, Brian M 

Sent: Thursday, October 17, 2019 3:58 PM
To: gpc-dev@listserv.kumc.edu 
Subject: Babel/ DROC 55 question


Hi everyone,



Can someone advise UIOWA on how to grab queries in Babel in XML and run them on 
our local i2b2 instance?  We have access to Babel and can copy the XML code for 
the DROC 55 request but can’t figure out how to transfer that logic and run 
counts.

Thanks,

Brian



Brian M. Gryzlak, MSW, MA

Project Coordinator

S414 CPHB

319.335.8218

The University of Iowa

Iowa City, IA 52242

brian-gryz...@uiowa.edu



Health Effectiveness Research Center 
(HERCe)


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gpc-dev 15 Oct agenda and meeting notes

[Dan Connolly]

What else for today's agenda?

Sorry for the delay; I got distracted yesterday...

UNMC is scheduled to scribe
https://docs.google.com/document/d/1ClOGXUgtOMP4vxCkpRYXfufgkt4tKusPP1msSf7kzWc/edit


Agenda snapshot:


  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in GoToMeeting preferences

*   GPC 
DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: UNMC

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   none this week???

*   
HackathonSeven
 notes are in progress

 *   Next meeting(s)/scribe: Oct 22 Scribe: 

*   Note scribe 
rotation
 appendix

  2.  CDM c7r1 due Monday, October 28th
FW: Data Curation Cycle 7 
updates   Roush, 
Steffani

 *   Status by site

*   SC/KUMC:

*   UIOWA

*   MCW:

*   MCRI:

*   UNMC

*   UTHSCSA

   *   Eric Moffett to share script to parallelize the running of 
modular code. Runs in ~4hs here. Done:

  *   UTHSCSA’s Concurrent Modular DCQ Run Instructions 
   Moffett, Eric 
E

*   UTSW: Nothing yet.

*   MU

*   IndianaU: Plans to start Mon., 10/14.

*   Utah:

*   Allina:

*   Intermountain:

  3.  #44 portable HERON ETL for 
NAACCR - is Docker 
close enough?

 *   DC: looking into the python3 stdbib (inc. sqlite3), followed by a 
little Java thing to shove the results into the DB 
naaccr-tumor-data/issues/25

 *   DC: UTSW, on a machine with your TR file, try (for <= 15 min) to run 
`docker run hello world` and tell me how it goes? 
https://docs.docker.com/get-started/
PR: ok.

 *   PR: does KUMC get one big file? Ours is in multiple parts
DC: I’ll add an issue for that and think about it.: 
naaccr-tumor-data/issues/26

  4.  Social Security Death Master file (SSDMF) distribution / hashing

 *   DC to follow up re MU


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gpc-dev 8 Oct agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

UTSW is scheduled to scribe
https://docs.google.com/document/d/1iGRtMHogyWSKreMcFEemSLX0VGqR5rc5jdEc5stcHKM/edit#


agenda snapshot:


Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in GoToMeeting preferences

*   GPC 
DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: UTSW

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   none this week

 *   Next meeting(s)/scribe: Oct 15 Scribe: UNMC? UTHSCSA?

*   Note scribe 
rotation
 appendix

  1.  Datavant walkthru / demo
Note slides Datavant Site Onboarding GPC Data Committee 
10012019.pdf​
 are now available, attached to GPC 
DataSecurity

  2.  CDM c7r1

 *   Reminder: DRN-OC forum Oct 7 11am 
ET

 *   FW: Data Curation Cycle 7 
updates   Roush, 
Steffani

 *   Lab Normal Value Processing 
   Phillip Reeder

 *   #752 
 cerner 
immunization query

 *   CDMV5.1 implementation is 
different!   
Campbell, James

 *   Populating the 
CDM   Gryzlak, 
Brian M

  3.  Project Outcomes Associated with 
Medication   
AINSLEY ELIZABETH HUFFMAN

  4.  #44 portable HERON ETL for 
NAACCR - is Docker 
close enough?

  5.  
HackathonSeven
 notes are in progress

  6.  
Milestone:text-notes-1

 *   Notes Extract 
Example   
Osinski, Kristen

  7.  How can I get access to babel.kumc.edu ? 
   Gryzlak, 
Brian M

  8.  Social Security Death Master file (SSDMF) distribution / hashing

 *   DC to follow up re MU


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portable NAACCR ETL: is Docker close enough?

[Dan Connolly]

At the hackathon, I talked about goals for portable NAACCR ETL 
(#44). UTSW was very 
interested in the idea of a single jar file. As much as I'd like to do that, in 
keeping with sticking with just the i2b2 platform (JVM, JDBC, ant) my 
exploratory work was in a python jupyter notebook and I ended up using python 
more than I had planned.

I have pretty much got it working on Docker 
(naaccr-tumor-data/issues/22).
 Is that close enough? Does UTSW use docker? Is ETL for NAACCR v18 enough 
motivation to start using it?

--
Dan

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HackathonSeven notes, in progress

[Dan Connolly]

Everybody is welcome to help take note or tweak them to clarify...
https://docs.google.com/document/d/14290PkEf_Q_Q7hzodldUq51NviDCsG4NrPIWyLsJ9q8/edit#

also linked from
https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonSeven#Records

--
Dan



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Re: Project Outcomes Associated with Medication

[Dan Connolly]

Several sites worked together on the Cancer RCR 
project where 
we looked at outcomes associated with medication using the CDM. For reference:
#651 Load infusion data to CDM v 4.0 med_admin table and 
submit

We also looked at medications in the breast cancer project, but that was using 
data from i2b2, not PCORNet CDM. ref 
#360, GPC Breast 
Cancer Second Data 
Pull
 slide presentation .

From: Gpc-dev  on behalf of AINSLEY 
ELIZABETH HUFFMAN 
Sent: Tuesday, October 1, 2019 9:35 AM
To: GPC-DEV@LISTSERV.KUMC.EDU 
Subject: Project Outcomes Associated with Medication


Hello,

We have an investigator at the University of Utah who is interested in looking 
at the effect of medication in disease management. Have any GPC sites had 
projects that examined outcomes associated with medication using the CDM?

Any information would be appreciated.

Thanks,

Ainsley E. Huffman, MS

Clinical Research Coordinator



Population Health Sciences | HSIR

295 Chipeta Way, RM 1N473

Salt Lake City, UT 84108

801-587-2093



[u_health_email]


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gpc-dev 1 Oct agenda and meeting notes (Datavant demo)

[Dan Connolly]

What else for tomorrow?

KUMC is scheduled to scribe
https://docs.google.com/document/d/15Ma51SeZXxf3DkdovuqaazaCzMrg2ojkAKdYtHcRU8s/edit

Agenda snapshot:


Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381<https://global.gotomeeting.com/meeting/join/817393381>; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in GoToMeeting preferences

*   GPC 
DevTeams<https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams> 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah 
(regrets: Holbrook), Allina, Intermountain

*   Today's scribe: KUMC

*   Welcome Jasmin Phua Head of Solutions, Health Systems & Government, 
Datavant

 *   Comments on the agenda? (ref 
SoftwareDev#tracking<https://informatics.gpcnetwork.org/trac/Project/wiki/SoftwareDev#tracking>)
 On last week’s notes? 
(#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12>)
Recent tickets 
opened/closed<https://informatics.gpcnetwork.org/trac/Project/timeline> - FYI 
(i.e. not intended for discussion)

*   none this week

 *   Next meeting(s)/scribe: Oct 8 Scribe: UTSW? UNMC?

*   Note scribe 
rotation<https://docs.google.com/document/d/15Ma51SeZXxf3DkdovuqaazaCzMrg2ojkAKdYtHcRU8s/edit#heading=h.zbjzupqx0rh7>
 appendix

*   
HackathonSeven<https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonSeven>
 is scheduled for October 2-3, 2019 in Kansas City

*   DataBuilder installation instructions OK? 
<http://listserv.kumc.edu/pipermail/gpc-dev/2019q3/005327.html>   Dan Connolly
Ref #335<https://informatics.gpcnetwork.org/trac/Project/ticket/335>, 
DataBuilder<https://informatics.gpcnetwork.org/trac/Project/wiki/DataBuilder> 
2157042460dc release; 
README<https://bitbucket.org/gpcnetwork/heron_extract/src/default/README.rst>

*   Reminder: DRN-OC forum Oct 7 11am 
ET<http://listserv.kumc.edu/pipermail/gpc-dev/2019q3/005332.html>

  1.  
Grouse-refresh-2<https://informatics.gpcnetwork.org/trac/Project/milestone/grouse-refresh-2>

 *   #727 Intermountain to send finder file to GDIT - done

 *   #733<https://informatics.gpcnetwork.org/trac/Project/ticket/733> 
GROUSE Refresh 2019 - 
UNMC<https://informatics.gpcnetwork.org/trac/Project/ticket/733> - ETA 
Mid-October

 *   #737<https://informatics.gpcnetwork.org/trac/Project/ticket/737> 
GROUSE Refresh 2019 - 
MCW<https://informatics.gpcnetwork.org/trac/Project/ticket/737> ETA 30 Sep

 *   #751<https://informatics.gpcnetwork.org/trac/Project/ticket/751> 
GROUSE Refresh 2019 - 
Indiana<https://informatics.gpcnetwork.org/trac/Project/ticket/751>: ETA 2 Oct

 *   #744<https://informatics.gpcnetwork.org/trac/Project/ticket/744> 
GROUSE Refresh 2019 - 
UTHSCSA<https://informatics.gpcnetwork.org/trac/Project/ticket/744> - ETA?

  2.  Datavant walkthru / demo

  3.  Lab Normal Value Processing 
<http://listserv.kumc.edu/pipermail/gpc-dev/2019q3/005324.html>   Phillip Reeder

  4.  How can I get access to babel.kumc.edu ? 
<http://listserv.kumc.edu/pipermail/gpc-dev/2019q3/005336.html>   Gryzlak, 
Brian M

  5.  Social Security Death Master file (SSDMF) distribution / hashing

 *   DC to follow up re MU


--
Dan

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Re: Data Quality Report - Cycle 6, Refresh 3 (July 2019)

[Dan Connolly]

Hi Susan,

Russ tells me cell size restrictions went away along with date shifting in the 
revised statement of work. He suggests contacting DRN-OC for the revised 
regulatory documents.

From: Gpc-dev  on behalf of Susan Rea 

Sent: Tuesday, September 24, 2019 11:46 AM
To: Hillary Sandoval ; GPC-DEV@LISTSERV.KUMC.EDU 
; 'Brittany Zschoche' 
Subject: RE: Data Quality Report - Cycle 6, Refresh 3 (July 2019)


Addressing the “Low Cell Count” Exception in the Data Curation Cycle 6, Third 
Refresh Performance Report:



I began to see query requests from the DRNOC recently asking to not suppress 
data for small cell sizes, and did not know why this change.  When I responded 
to the Query Fulfillment team to say that we had local governance for 
suppressing small cell sizes, they said:



Thank you for your question.  The PMP program allows for you to update the 
masking parameter as required by your DM/CRN's governance.  The default is 0, 
or no masking, given the CRN contract language around masking of cell counts.



Can someone point out the GPC contract language and whether that might be 
included in our current DSA with GPC?  I need the provenance of this change in 
order to process downstream with our specific compliance team (Cybersecurity) 
for responding to de-identified data queries via PopMedNet.  I think this might 
fit into the conversations as we process the new PCORnet DSA V3.0



Meantime, we have to suppress small cell sizes per original PCORnet local 
compliance agreements.



Thanks so much,

Susan Rea

CDM Data Administrator

Intermountain Healthcare



From: Gpc-dev  On Behalf Of Hillary Sandoval
Sent: Monday, September 16, 2019 9:08 AM
To: GPC-DEV@LISTSERV.KUMC.EDU; 'Brittany Zschoche' 

Subject: Data Quality Report - Cycle 6, Refresh 3 (July 2019)



WARNING: Stop. Think. Read. This is an external email.

Hello everyone,



Please find attached the Data Quality report from PCORnet based on data 
curation responses for Cycle 6, refresh 3 (July 2019). This will be discussed 
on the Dev call tomorrow and there will be opportunity for questions, etc. so 
please review prior to the call.



Thank you,



Hillary Sandoval

Project Manager, Center for Medical Informatics and Enterprise Analytics

University of Kansas Medical Center

hsando...@kumc.edu

913-588-7205



Request Help 
Here

www.kumc.edu/ea-mi

www.gpcnetwork.org



NOTICE: This e-mail is for the sole use of the intended recipient and may 
contain confidential and privileged information. If you are not the intended 
recipient, you are prohibited from reviewing, using, disclosing or distributing 
this e-mail or its contents. If you have received this e-mail in error, please 
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Re: [External] Re: How can I get access to babel.kumc.edu ?

[Dan Connolly]

You can get some site-level aggregate data by browsing the terms and looking at 
the counts there.

But there is no patient data of any sort on babel. Any query you run will give 
0 results (or errors or something).
But you can take that query and put it in a shared folder for someone else to 
run at their site.

What are you trying to do?

Have you considered using ACT SHRINE?

From: Gryzlak, Brian M 
Sent: Friday, September 27, 2019 1:51 PM
To: Dan Connolly ; gpc-dev@listserv.kumc.edu 

Subject: RE: [External] Re: How can I get access to babel.kumc.edu ?


Is there a tutorial that demonstrates how to use Babel to return site-level 
aggregate data?

Brian



From: Dan Connolly 
Sent: Friday, September 27, 2019 12:50 PM
To: Gryzlak, Brian M ; gpc-dev@listserv.kumc.edu
Subject: [External] Re: How can I get access to babel.kumc.edu ?



The password request button at the top takes you to a page that says "To get a 
babel account, contact one of the account 
representatives<https://protect-us.mimecast.com/s/lV79CR605DurpgWZC9wmjK?domain=babel.gpcnetwork.org>
 (e.g. from your site)." I recently cleaned up the site account reps as part of 
HackathonSeven<https://protect-us.mimecast.com/s/bK1yCVOk0KFlEPyQtzUYfZ?domain=informatics.gpcnetwork.org>
 prep; Nick used to be the UIOWA site rep. I'm adding you in his place...

added: Gryzlak, Brian M

Now you should be able to give out accounts by using the site rep admin page:
https://babel.gpcnetwork.org/cgi-bin/babelaccess.py/rep_admin<https://protect-us.mimecast.com/s/KGKrCW6ljXujQyqoCKz4fL?domain=babel.gpcnetwork.org>

The thing is a little wonky; granting an account is separate from issuing a 
password, which you do by doing an account reset on their behalf:
https://babel.gpcnetwork.org/cgi-bin/babelaccess.py/<https://protect-us.mimecast.com/s/MXz5CXD0k2IngMKrCkJy_1?domain=babel.gpcnetwork.org>

I can give a demo on Tuesday if it's still not clear.



From: Gpc-dev 
mailto:gpc-dev-boun...@listserv.kumc.edu>> 
on behalf of Gryzlak, Brian M 
mailto:brian-gryz...@uiowa.edu>>
Sent: Friday, September 27, 2019 12:38 PM
To: gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu> 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: How can I get access to babel.kumc.edu ?







Brian M. Gryzlak, MSW, MA

Project Coordinator

S423 CPHB

319.335.8218

The University of Iowa

Iowa City, IA 52242

brian-gryz...@uiowa.edu<mailto:brian-gryz...@uiowa.edu>



Health Effectiveness Research Center 
(HERCe)<http://protect-us.mimecast.com/s/gC42CYEnlNi3v6lBhMYZYI?domain=public-health.uiowa.edu>


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Re: How can I get access to babel.kumc.edu ?

[Dan Connolly]

The password request button at the top takes you to a page that says "To get a 
babel account, contact one of the account 
representatives 
(e.g. from your site)." I recently cleaned up the site account reps as part of 
HackathonSeven
 prep; Nick used to be the UIOWA site rep. I'm adding you in his place...

added: Gryzlak, Brian M

Now you should be able to give out accounts by using the site rep admin page:
https://babel.gpcnetwork.org/cgi-bin/babelaccess.py/rep_admin

The thing is a little wonky; granting an account is separate from issuing a 
password, which you do by doing an account reset on their behalf:
https://babel.gpcnetwork.org/cgi-bin/babelaccess.py/

I can give a demo on Tuesday if it's still not clear.


From: Gpc-dev  on behalf of Gryzlak, Brian M 

Sent: Friday, September 27, 2019 12:38 PM
To: gpc-dev@listserv.kumc.edu 
Subject: How can I get access to babel.kumc.edu ?






Brian M. Gryzlak, MSW, MA

Project Coordinator

S423 CPHB

319.335.8218

The University of Iowa

Iowa City, IA 52242

brian-gryz...@uiowa.edu



Health Effectiveness Research Center 
(HERCe)


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Re: [External] HASH_TOKEN and Datavant

[Dan Connolly]

Hi Brian,

I expect all will be revealed next week (Oct 1) when DataVant does their demo / 
walthru.

Jas, bonus points if you want to share anything by email in advance.

--
Dan



From: Gpc-dev  on behalf of Gryzlak, Brian M 

Sent: Tuesday, September 24, 2019 11:25 AM
To: Mazumder, Narayana ; 
gpc-dev@listserv.kumc.edu 
Subject: RE: [External] HASH_TOKEN and Datavant


Hi everyone,



Is there any guidance available on how to population HASH_TOKEN, or do we 
expect that will come out with the refresh query?  I see mention of different 
“token strategies” in the CDM 5.0 
spec
 but I’m not sure where to find info about those approaches.

Thanks,

Brian



Brian M. Gryzlak, MSW, MA

Project Coordinator

S423 CPHB

319.335.8218

The University of Iowa

Iowa City, IA 52242

brian-gryz...@uiowa.edu



Health Effectiveness Research Center 
(HERCe)

From: Gpc-dev  On Behalf Of Mazumder, 
Narayana
Sent: Monday, September 9, 2019 3:36 PM
To: gpc-dev@listserv.kumc.edu
Subject: [External] HASH_TOKEN and Datavant



Hi Team,



Has anyone worked on the CDM HASH_TOKEN table? From the description in CDM 5.0 
specification, it looks like we are supposed to use the PRIVATE_DEMOGRAPHIC 
table to create tokens.



Also, are we supposed to download the Datavant send module from somewhere and 
use it to create tokens?



Thank you,

Narayana





Narayana Mazumder

Research Informatics Analyst – Ld / Data Architect

Clinical Research Informatics and Analytics

Allina Commons | 2925 Chicago Ave S | Minneapolis, MN 55407

612.262.6010 | narayana.mazum...@allina.com



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DataBuilder installation instructions OK?

[Dan Connolly]

Yesh,

You asked about DataBuilder installation documentation. Is the 
README 
good enough?

For reference: 
DataBuilder 
2157042460dc release, 
#335.


I guess there's no urgency to this, so I'm taking it off the dev call agenda 
until you have news for us.

--
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Re: Lab Normal Value Processing

[Dan Connolly]

In our CDM, we don't seem to use normal ranges from individual results (yet) 
either; we us an age/sex adjusted table:
https://github.com/kumc-bmi/i2p-transform/blob/db7cf8809d810385d2e6d4e4f1e66ac7cb02ed57/curated_data/labnormal.csv
https://github.com/kumc-bmi/i2p-transform/blob/master/Oracle/lab_result_cm.sql

In i2b2, we do mark Hi / Lo results on an individual basis, but it looks like 
we filter out things other than plain numbers.
https://github.com/kumc-bmi/heron/blob/master/heron_load/epic_labs_transform.sql
 (private repository; see 
MultiSiteDev 
regarding access)

FWIW, there is some regular expression stuff in there to handle result values 
such as ">40". It also uses
 
https://github.com/kumc-bmi/heron/blob/master/heron_load/curated_data/lab_regex.csv




From: Gpc-dev  on behalf of Phillip Reeder 

Sent: Tuesday, September 24, 2019 9:36 AM
To: gpc-dev@listserv.kumc.edu 
Subject: Lab Normal Value Processing


We haven’t used the normal values associated with individual lab results in the 
past and while looking at the normal values, many of them are text with 
modifiers like <,> <=. Etc., along with some that are ranges like  1.0-10.0.   
Does anyone have SQL/regular expressions that will filter all of those out into 
the columns required for the PCORICDM?



Thanks,

Phillip





UT Southwestern

Medical Center

The future of medicine, today.
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gpc-dev 24 Sep agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

Intermountain is scheduled to scribe.
https://docs.google.com/document/d/1NqHOoHZMnAKsrIh86ZFOZvBDViI2T84RfrOWHJ9pr0o/edit#
[https://lh4.googleusercontent.com/2RTGeNuZpl4VkAOnXzTIqisK8ppUWDumxcIE_0RzaP91JeweCAD-Ta1WAGyD0T9aY5guXg=w1200-h630-p]
24 Sep GPC-DEV Meeting 
Notes
Convene, take roll, review records and plan next meeting(s) 11:00 a.m. Central 
Time.\u000B​Meeting ID and access code: 817-393-381; call +1 (571) 317-3131 
Roll; Reminder - put site after your name in GoToMeeting preferences GPC 
DevTeams represented? KUMC, UIOWA, MCW, MCRI, UNMC, UTHSCSA, UTSW, MU, In...
docs.google.com


agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in GoToMeeting preferences

*   GPC 
DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: Intermountain

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   none this week

 *   Next meeting(s)/scribe: Oct 1 Scribe: KUMC? UTSW?

*   Note scribe 
rotation
 appendix

  2.  Datavant walkthru / demo - scheduled for 1 Oct

  3.  Data Quality Report - Cycle 6, Refresh 3 (July 
2019)   Hillary 
Sandova

 *   Steffani to investigate the possibility of DRNOC representatives 
joining a future GPC-dev call

 *   Steffani to follow up with DRNOC regarding what sites are required to 
do balancing demands with available source data

  4.  
HackathonSeven
 is scheduled for October 2-3, 2019 in Kansas City

 *   Please fill out the Final LEC/Hackathon Meal Headcounts 
survey by noon on Tuesday, 
September 24th

  5.  DataBuilder release, deployment 
(#335)

 *   
DataBuilder 
2157042460dc release: 
README 
provides sufficient installation info for UNMC?

  6.  
Grouse-refresh-2

 *   #744 
GROUSE Refresh 2019 - 
UTHSCSA - ETA 21 Sep

 *   #751 
GROUSE Refresh 2019 - 
Indiana: ETA 24 Sep

 *   #737 
GROUSE Refresh 2019 - 
MCW ETA 30 Sep

 *   #733 
GROUSE Refresh 2019 - 
UNMC - adding 
birthdate column to crosswalk - ETA?

  7.  
Milestone:tumor-reg-18

 *   #739 HERON 
NAACCR ETL outdated by 
v18: taking 
kumc-bmi/naaccr-tumor-data to 
production…

  8.  Social Security Death Master file (SSDMF) distribution / hashing

 *   DC to follow up re MU - done?

--
Dan

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gpc-dev 17 Sep agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

MCW is scheduled to scribe
https://docs.google.com/document/d/1BR0L8GPt-5qNn0tKonuZ0JVF8DNdvI0nYYWHykJ8OAo/edit#

agenda snapshot:

  1.  Convene, take roll, review records and plan next meeting(s)

 *   11:00 a.m. Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   Roll; Reminder - put site after your name in GoToMeeting preferences

*   GPC 
DevTeams 
represented? KUMC, UIOWA, MCW, MCRI,  UNMC, UTHSCSA, UTSW, MU, IndianaU, Utah, 
Allina, Intermountain

*   Today's scribe: MCW

 *   Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   none this week

 *   Next meeting(s)/scribe: Sep 24 Scribe: Allina? KUMC?

*   Note scribe 
rotation
 appendix

  2.  DataBuilder release, deployment

 *   
DataBuilder 
2157042460dc release: 
README 
provides sufficient installation info?

  3.  
Grouse-refresh-2

 *   #751 
GROUSE Refresh 2019 - 
Indiana: 24 Sep 
feasible?

 *   #733 
GROUSE Refresh 2019 - 
UNMC - adding 
birthdate column to crosswalk

 *   #737 
GROUSE Refresh 2019 - 
MCW birthdate 
crosswalk

 *   #744 
GROUSE Refresh 2019 - 
UTHSCSA - LP 
looking into it

  4.  
Milestone:tumor-reg-18
 due Sep 5

 *   #739 HERON 
NAACCR ETL outdated by 
v18: taking 
kumc-bmi/naaccr-tumor-data to 
production…

  5.  
HackathonSeven
 is scheduled for October 1st & 2nd, 2019 in Kansas City - note session 
descriptions etc.

  6.  Cerner Scripts for 
CDM   Manuel, 
Laura S M

--
Dan

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