gpc-dev / Cancer RCR 21 Nov agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   21 Nov shared meeting 
ntoes
 *   scribe: UTHSCSA, presuming the offer still holds

snapshot:




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

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

 *   Roll: Reminder - put institution after your name in GoToMeeting 
preferences

*   all 12 GPC 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF/MCRI, UMN, UNMC, UTHSCSA, UTSW, 
MU, IU

*   Cancer RCR project sites? UFL, VUMC, MUSC, LSU

*   Today's scribe: UTHSCSA?

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

*   #669 (LSU - Complete Cancer RCR Aim 1 Task 1.A., 1.B, 1.C, 1.E 
surveys) closed

*   #674 (Submit final code lists to coordinating center for PCORnet 
queries) created

*   #632 (Specimen source to LOINC mapping-Nebraska(UNMC)) 
closed

*   #568 (Response on BABEL is painfully slow) 
closed

*   #567 (SNOW spoke server implementation for KUMC) 
closed

*   #604 (snow shrine prod hub public cert renewal - spoke server 
keystore updates) 
closed

 *   Next meeting(s):  28 Nov scribe: ???

*   Note LRU scribe schedule in 
#12

  2.  HackathonFive 
Registration by 
Jan 12
details sufficient to justify air fare due at T-8 weeks = Dec 18, 2017

  3.  
Milestone:cancer-rcr-1
 due Nov 27

 *   FYI: Global RCR Meeting Nov 
14
 meeting notes

 *   #672 DUAs 
for non-GPC sites in support of RCR 
work

*   Christine to share IRB approval with 
brian-gryz...@uiowa.edu, MUSC

 *   #673 
Respond to Aim 1 Survey 
feedback / 
Site-by-site 
feedback

*   IU

*   KUMC

   *   #675 (regulatory approval to select Cancer RCR cohort by real DX 
dates?) created

*   MCRF asks for example of molecular test

   *   see BRCA1, 2 etc. in 
#667

*   MCW - answers look complete

*   MU - for Mosa to look into

*   MUSC - answers look complete

*   UFL - answers look complete

*   UIOWA

*   UMN - real dates? (other answers look complete)

*   UNMC: Jay Pedersen to follow up

   *   “We  have found 865 distinct HCPCS codes, including 179 distinct 
'J' codes.

However, this did not include the J9355 code.” - Pedersen 13 
Nov

*   UTSW: answers look complete modulo regulatory #675 (“planning to 
have the data refreshed on Dec.15 for I2b2. CDM DB needs few days to update”)

   *   HCPCS Codes in 
Epic   Phillip 
Reeder

*   VUMC - real dates “in progress”; other answers look complete

*   LSU?

 *   #666 
Review of EDC reports site survey responses on data 
holdings done?

*   #665 
EDC reports done 
(aside from LSU)

 *   #659 
Develop process for non-GPC sites to transfer data to 

RE: [gpc-informatics] #659: Develop process for non-GPC sites to transfer data to UIOWA

[Dan Connolly]

Let's see... my working notes* show the cohort (folks in the registry with a 
solid tumor... #652) has 20K patients. For NAACCR data (#655) I see roughly the 
same number of tumors. That's a somewhat large number of records to import into 
a REDCap CRF, but probably not infeasible.

Of the 12 CDM tables we're collecting (#656), I'll grab DIAGNOSIS somewhat 
arbitrarily... I get 3.7M records for this cohort.

select count(*)
from pcornet_cdm.diagnosis
where patid in (
  select distinct patient_num from rcr_cohort
)
;

I shudder at the thought of uploading that many records into a REDCap CRF. 
Plus, the CDM tables have been through quite a bit of QA, so I'd be more 
confident about having sites submit a .zip of CSV files, either attached to a 
REDCap survey or CRF or using something like securefiles.kumc.edu.


* I just attached my working notes as 
https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/652/cancer-rcr-drugs.sql

-- 
Dan


From: Gryzlak, Brian M [brian-gryz...@uiowa.edu]
Sent: Thursday, November 09, 2017 3:06 PM
To: Dan Connolly; gpc-dev@listserv.kumc.edu; Tamara McMahon
Subject: RE: [gpc-informatics] #659: Develop process for non-GPC sites to 
transfer data to UIOWA

Thanks Dan - BTW - do you have a general sense of the max # of records that 
sites were asked to upload into those redcap tables?  E.g., 1,000? 10,000?  
100,000?



-Original Message-
From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Thursday, November 9, 2017 3:01 PM
To: Gryzlak, Brian M <brian-gryz...@uiowa.edu>; gpc-dev@listserv.kumc.edu; 
Tamara McMahon <tmcma...@kumc.edu>
Subject: RE: [gpc-informatics] #659: Develop process for non-GPC sites to 
transfer data to UIOWA

We could only give you access if you're on the study team for UIOWA IRB 
protocol 201501798.

Meanwhile, I made a copy of the first one less the data and gave you access:
https://redcap.gpcnetwork.org/redcap_v6.11.5/UserRights/index.php?pid=87

For the second one, I'm attaching the data dictionary; that should let you 
import it into UIOWA's REDCap if you want to play with it.

--
Dan


From: Gryzlak, Brian M [brian-gryz...@uiowa.edu]
Sent: Thursday, November 09, 2017 2:03 PM
To: gpc-dev@listserv.kumc.edu; Dan Connolly; Tamara McMahon
Subject: RE: [gpc-informatics] #659: Develop process for non-GPC sites to 
transfer data to UIOWA

OK thanks - Tamara - any chance I can get read-access to the redcap projects 
that are cited?
https://redcap.gpcnetwork.org/redcap_v6.11.5/index.php?pid=32
https://redcap.gpcnetwork.org/redcap_v6.11.5/index.php?pid=64

Brian


-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Thursday, November 9, 2017 1:58 PM
To: Gryzlak, Brian M <brian-gryz...@uiowa.edu>; dconno...@kumc.edu
Subject: Re: [gpc-informatics] #659: Develop process for non-GPC sites to 
transfer data to UIOWA

#659: Develop process for non-GPC sites to transfer data to UIOWA
--+---
 Reporter:  bgryzlak  |   Owner:  bgryzlak
 Type:  problem   |  Status:  new
 Priority:  major |   Milestone:  cancer-rcr-1
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:
 Blocking:  660   |
--+---
Changes (by dconnolly):

 * cc: dconnolly, bmcdowell (added)


Comment:

 Brian writes:
 > Brad noted that whatever mechanism you set up for the second data  transfer 
 > of breast cancer data to KUMC for the breast cancer project  worked 
 > relatively well.  What mechanism did you use that allowed for data  checks?  
 > A redcap project?

 Yes, a REDCap project. (A couple of them, actually.) See links to the  REDCap 
projects along with an Oct 4, 2016 slide presentation etc. in
 ticket:297#comment:28

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/659#comment:2>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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RE: [gpc-informatics] #659: Develop process for non-GPC sites to transfer data to UIOWA

[Dan Connolly]

We could only give you access if you're on the study team for UIOWA IRB 
protocol 201501798.

Meanwhile, I made a copy of the first one less the data and gave you access:
https://redcap.gpcnetwork.org/redcap_v6.11.5/UserRights/index.php?pid=87

For the second one, I'm attaching the data dictionary; that should let you 
import it into UIOWA's REDCap if you want to play with it.

-- 
Dan


From: Gryzlak, Brian M [brian-gryz...@uiowa.edu]
Sent: Thursday, November 09, 2017 2:03 PM
To: gpc-dev@listserv.kumc.edu; Dan Connolly; Tamara McMahon
Subject: RE: [gpc-informatics] #659: Develop process for non-GPC sites to 
transfer data to UIOWA

OK thanks - Tamara - any chance I can get read-access to the redcap projects 
that are cited?
https://redcap.gpcnetwork.org/redcap_v6.11.5/index.php?pid=32
https://redcap.gpcnetwork.org/redcap_v6.11.5/index.php?pid=64

Brian


-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Thursday, November 9, 2017 1:58 PM
To: Gryzlak, Brian M <brian-gryz...@uiowa.edu>; dconno...@kumc.edu
Subject: Re: [gpc-informatics] #659: Develop process for non-GPC sites to 
transfer data to UIOWA

#659: Develop process for non-GPC sites to transfer data to UIOWA
--+---
 Reporter:  bgryzlak  |   Owner:  bgryzlak
 Type:  problem   |  Status:  new
 Priority:  major |   Milestone:  cancer-rcr-1
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:
 Blocking:  660   |
--+---
Changes (by dconnolly):

 * cc: dconnolly, bmcdowell (added)


Comment:

 Brian writes:
 > Brad noted that whatever mechanism you set up for the second data  transfer 
 > of breast cancer data to KUMC for the breast cancer project  worked 
 > relatively well.  What mechanism did you use that allowed for data  checks?  
 > A redcap project?

 Yes, a REDCap project. (A couple of them, actually.) See links to the  REDCap 
projects along with an Oct 4, 2016 slide presentation etc. in
 ticket:297#comment:28

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/659#comment:2>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
"Variable / Field Name","Form Name","Section Header","Field Type","Field Label","Choices, Calculations, OR Slider Labels","Field Note","Text Validation Type OR Show Slider Number","Text Validation Min","Text Validation Max",Identifier?,"Branching Logic (Show field only if...)","Required Field?","Custom Alignment","Question Number (surveys only)","Matrix Group Name","Matrix Ranking?","Field Annotation"
record_id,medication_exposure,,text,"Record ID",,"suggested format: StudyID_exposure start_instance num",,,
study_id,medication_exposure,,text,"Study ID"y,
exposure_start,medication_exposure,,text,"Date, time of start of exposure",,,datetime_ymd,,,y,,y,
exposure_end,medication_exposure,,text,"Date, time of end of exposure",,,datetime_ymd,,,y,,,
va_class,medication_exposure,,dropdown,"VA Classification","AN000, [AN000] ANTINEOPLASTICS | AN100, [AN100] ANTINEOPLASTICS,ALKYLATING AGENTS | AN200, [AN200] ANTINEOPLASTIC ANTIBIOTICS | AN300, [AN300] ANTINEOPLASTICS,ANTIMETABOLITES | AN400, [AN400] ANTINEOPLASTIC ADJUVANTS | AN500, [AN500] ANTINEOPLASTIC HORMONES | AN600, [AN600] ANTINEOPLASTIC RADIOPHARMACEUTICALS | AN700, [AN700] PROTECTIVE AGENTS | AN900, [AN900] ANTINEOPLASTIC,OTHER | HS000, [HS000] HORMONES/SYNTHETICS/MODIFIERS | HS100, [HS100] ANDROGENS/ANABOLICS | HS200, [HS200] CONTRACEPTIVES,SYSTEMIC | HS300, [HS300] ESTROGENS | HS400, [HS400] GONADOTROPINS | HS500, [HS500] BLOOD GLUCOSE REGULATION AGENTS | HS501, [HS501] INSULIN | HS502, [HS502] ORAL HYPOGLYCEMIC AGENTS,ORAL | HS503, [HS503] ANTIHYPOGLYCEMICS | HS509, [HS509] HYPOGLYCEMIC AGENTS,OTHER | HS600, [HS600] PARATHYROID | HS700, [HS700] PITUITARY | HS701, [HS701] ANTERIOR PITUITARY | HS702, [HS702] POSTERIOR PITUITARY | HS800, [HS800] PROGESTINS | HS850, [HS850] THYROID MODIFIERS | HS851, [HS851] THYROID SUPPLEMENTS | HS852, [HS852] ANTITHYROID AGENTS | HS875, [HS875] PROSTAGLANDINS | HS900, [HS900] HORMONES/SYNTHETICS/MODIFIERS,OTHER | HS050, [HS050] ADRENAL CORTICOSTEROIDS | HS051, [HS051] GLUCOCORTICOIDS | HS052, [HS052] MINERALOCORTICOIDS","This is redundant w.r.t. rxcui and can be filled in later but might be handy for summarizing data.",autocomplete,,
rxcui,medication_exposure,,dropdown,"Medication (RxNorm)","377179, [AN100] RXCUI:377179 Busulfan Injectable Solution | 371165, [AN100] RXCUI:371165 Busulfan Oral Tablet | 378774, [AN100] RXCUI:

RE: regulatory approval to select by real DX dates? RE: RCR Aim 1 survey feedback - site responses requested

[Dan Connolly]

The list of CDM tables in 
ticket:656#comment:2<https://informatics.gpcnetwork.org/trac/Project/ticket/656#comment:2>
 answers my question: yes, we're reporting lots of other dates.

--
Dan


From: Dan Connolly
Sent: Tuesday, November 07, 2017 9:45 AM
To: Gryzlak, Brian M; gpc-...@listserv.kumc.edu; ,; Tamara McMahon
Cc: Russ Waitman
Subject: regulatory approval to select by real DX dates? RE: RCR Aim 1 survey 
feedback - site responses requested

Tamara, would you please ask Karen B. about this? Russ just happened to be in 
the office after his class; he had a suggestion, but he wasn't quite sure and 
asked that you consult Karen...

I see "Verify that you will use real diagnosis dates to select cohort" in the 
feedback items. I don't see "limited" in the 
CancerRCR<https://informatics.gpcnetwork.org/trac/Project/wiki/CancerRCR> 
project plan and I'm not aware of an approved IRB protocol.

Russ suggested that since we're only using year to select the cohort, that 
should fall under de-identified. I reminded him of the screw case where we 
include Patient 123 in the 2013-2016 cohort, but we also report Dec 30, 2017 as 
the start_date of the primary site observation (the ETL code uses diagnosis 
date in this case), which reveals the date_shift for patient 123 to be exactly 
-364, which gives away the real dates corresponding to all shifted dates.

Brad, Brian, Nick, if no other dates are collected, this issue goes away. From 
a technical perspective, it would be easier to confirm if I could see the query 
for building the dataset 
(#655<https://informatics.gpcnetwork.org/trac/Project/ticket/655>).

--
Dan


From: Gpc-rcr [gpc-rcr-boun...@listserv.kumc.edu] on behalf of Gryzlak, Brian M 
[brian-gryz...@uiowa.edu]
Sent: Tuesday, November 07, 2017 9:17 AM
To: gpc-...@listserv.kumc.edu; ,
Subject: [Gpc-rcr] RCR Aim 1 survey feedback - site responses requested

Hi everyone,

Thanks again to the sites that responded to the Aim 1 surveys.  The RCR 
executive committee has reviewed your responses.

Site-by-site feedback is now posted 
here.<https://docs.google.com/document/d/143B8BzwJm4JsE3y00H8fpKaOlrDNuX80sZ29IqSdKDI/edit?usp=sharing>
 We are requesting that all sites please review the feedback and respond to 
each item in the ‘Response’ columns (NAACCR and CDM data).

Thanks,
Brian

PS - Item for today's dev call

Brian M. Gryzlak, MSW, MA
Project Coordinator
2127 Westlawn  319.335.4897 (primary)
S533 Pharmacy  319.353.3857
The University of Iowa
Iowa City, IA 52242
brian-gryz...@uiowa.edu<mailto:brian-gryz...@uiowa.edu>

Health Effectiveness Research Center 
(HERCe)<http://www.public-health.uiowa.edu/herce/>
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regulatory approval to select by real DX dates? RE: RCR Aim 1 survey feedback - site responses requested

[Dan Connolly]

Tamara, would you please ask Karen B. about this? Russ just happened to be in 
the office after his class; he had a suggestion, but he wasn't quite sure and 
asked that you consult Karen...

I see "Verify that you will use real diagnosis dates to select cohort" in the 
feedback items. I don't see "limited" in the 
CancerRCR 
project plan and I'm not aware of an approved IRB protocol.

Russ suggested that since we're only using year to select the cohort, that 
should fall under de-identified. I reminded him of the screw case where we 
include Patient 123 in the 2013-2016 cohort, but we also report Dec 30, 2017 as 
the start_date of the primary site observation (the ETL code uses diagnosis 
date in this case), which reveals the date_shift for patient 123 to be exactly 
-364, which gives away the real dates corresponding to all shifted dates.

Brad, Brian, Nick, if no other dates are collected, this issue goes away. From 
a technical perspective, it would be easier to confirm if I could see the query 
for building the dataset 
(#655).

--
Dan


From: Gpc-rcr [gpc-rcr-boun...@listserv.kumc.edu] on behalf of Gryzlak, Brian M 
[brian-gryz...@uiowa.edu]
Sent: Tuesday, November 07, 2017 9:17 AM
To: gpc-...@listserv.kumc.edu; ,
Subject: [Gpc-rcr] RCR Aim 1 survey feedback - site responses requested

Hi everyone,

Thanks again to the sites that responded to the Aim 1 surveys.  The RCR 
executive committee has reviewed your responses.

Site-by-site feedback is now posted 
here.
 We are requesting that all sites please review the feedback and respond to 
each item in the ‘Response’ columns (NAACCR and CDM data).

Thanks,
Brian

PS - Item for today's dev call

Brian M. Gryzlak, MSW, MA
Project Coordinator
2127 Westlawn  319.335.4897 (primary)
S533 Pharmacy  319.353.3857
The University of Iowa
Iowa City, IA 52242
brian-gryz...@uiowa.edu

Health Effectiveness Research Center 
(HERCe)
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gpc-dev / Cancer RCR 7 Oct agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev shared notes 7 
Oct;
 scribe: MU

current snapshot:




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

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

 *   Roll: Reminder - put institution after your name in GoToMeeting 
preferences

*   all 12 GPC 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF/MCR, UMN, UNMC, UTHSCSA, UTSW, 
MU, IU

*   Cancer RCR project sites? UFL, VUMC, MUSC, LSU

*   Today's scribe: MU

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

*   #570 (collect expanded obesity cohort data: demographics, income, 
insurance / ...) 
closed 
fixed

   *   #140 (socio-economic status based on geographic context) 
closed 
fixed

   *   #379 (Link EHR data to Health and Medical Research Family Survey 
(HMRFS) 2 ...) 
closed 
fixed

 *   Next meeting(s):  14 Nov, scribe?

*   Note LRU scribe schedule in 
#12

*   Global RCR 
Meeting 
Nov 14

  2.  
Milestone:cancer-rcr-1
 due Nov 20

 *   Thanks to sites that completed the surveys:
#645 (Complete REDCap survey for NAACCR solid tumor data - RCR Aim 1 Task 1.A.) 
closed 
fixed
#648 (Complete REDCap survey for CDM billing data - RCR Aim 1 Task 1.B.) 
closed 
fixed
#649 (Complete REDCap survey for CDM test /med data - RCR Aim 1 Tasks 1.C and 
...) 
closed 
fixed
#668 (UMN - Complete Cancer RCR Aim 1 Task 1.A., 1.B, 1.C, 1.E 
surveys) closed 
fixed

 *   #669 (LSU - Complete Cancer RCR Aim 1 Task 1.A., 1.B, 1.C, 1.E 
surveys) created

 *   #666 
Review of EDC reports site survey responses on data holdings
Executive Committee 
results … survey results document
Brian
 -- Have more details by dev call next week (7 Nov)

 *   #665 EDC 
reports
specifically 
looking for 4.G RXNORM mapping
GPC Redcap project: PCORNet CDM Empirical Data Characterization (EDC) report 
sharing
UFL, VUMC, MUSC, LSU - 
please provide Table IV from your most recent EDC report to 
brian-gryz...@uiowa.edu

 *   #656 CDM: 
Finalize specifications on which CDM tables to pull and provide guidance to 
sites

*   (Brian / Brad) CDM tables - we will have a response on which CDM 
tables will be requested from RCR sites on the 7 NOV dev call.

 *   #650 
Guidance to sites on loading infusion data
Nick, is the 
guidance Russ gave good enough?

 *   #660 (Pull and submit tumor analysis dataset and CDM tables for cohort 
(1st ...) created

*   Last week:
Brian will update the Aim 1 Task List 

 by COB on 10/31 to clarify RCR tasks (including items discussed on this dev 
call).
Brian will send an email to the RCR list to confirm this was done.

   *   Done: [Gpc-rcr] RCR project 
updates   
Gryzlak, Brian M

*   

gpc-dev / RCR 24 Oct agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 24 Oct shared 
notes;
 scribe: UIOWA

current snapshot:




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

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

 *   Roll: Reminder - put institution after your name in GoToMeeting 
preferences

*   all 12 GPC 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF/MCRI, UMN, UNMC, UTHSCSA, UTSW, 
MU, IU

*   Today’s meeting is joint with the Cancer RCR project:
UF, MUSC, VUMC

*   today's scribe: UIOWA

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

*   GPC LEC 16-17 Oct session 
notes, posters available

*   #326 (Quality checks for terminology alignment (with fact volume) 
for GPC ...) closed 
 invalid

*   #282 (check correlation of GPC enrollment data with CDM ENR_BASIS) 
closed 
wontfix

*   #625 (Disk space allocation and LVM setup for SNOW SHRINE spoke 
server(s)) 
closed 
fixed

*   #647 (Send copy of Oct 2017 CDM to KUMC for Cancer RCR integration 
testing) created

 *   Next gpc-dev meeting:  31 Oct; scribe: ???

*   Note LRU scribe schedule in 
#12

*   Global RCR 
Meeting 
Nov 14 - agenda in preparation

*   
HackathonFive
 dates resolved: Feb 12-13, 2018

   *   details sufficient to justify air fare due at T-8 weeks = Dec 
18, 2017
detailed agenda due at T-2 weeks = Jan 29, 2018

  2.  Reminder: DRNOC invites CDM 4 draft feedback; send feedback to 
dr...@pcornet.org through 31 Oct.

  3.  
Milestone:cancer-rcr-1
 due 25 Oct
Cancer RCR Aim 
1
 schedule spreadsheet; RCR listserv: 
gpc-rcr

 *   #645 
Complete REDCap survey for NAACCR solid tumor data - RCR Aim 1 Task 1.A.
#648
 Complete REDCap survey for CDM billing data - RCR Aim 1 Task 1.B.
#649
 Complete REDCap survey for CDM test /med data - RCR Aim 1 Tasks 1.C and 
1.E

*   Nick to send REDCap surveys
Done: [Gpc-rcr] Aim 1 
surveys

*   Status by site (updated by Brian G as of 3pm on 10/23) - Please aim 
to complete any remaining surveys by COB on 10/25/17

   *   KUMC: done: submitted all 3
#640  
closed duplicate

   *   IU - 1A done

   *   LSU -

   *   MCRF - All 3 done

   *   MCW - All 3 done

   *   MU - adone, bdone

   *   MUSC - All 3 done

   *   UF - All 3 done

   *   UIOWA - 1.A done, 1.B done

   *   UMN -

   *   UNMC - submitted 1.A NAACR

   *   UTSW - All 3 done

   *   VUMC - 1A done, b and c/e in process

*   How to interpret “All cases thru 2016”? Dan C. 
ticket:645#comment:5

 *   Next steps: (Brian to describe by meeting time)

 *   Putting med info in CDM (row 6)
RW: to meet with Keith M. of DRN OC done:
[Gpc-rcr] using Cancer RCR project for testing CDM 4.0 medadmin 
table   
Russ Waitman

*   Brian G organizing meeting on Med Administration
Done; meeting notes: Medications and CDM for 

RE: SNOW Shrine Hub

[Dan Connolly]

You might review the relevant design issue ticket:

#332 How to deal with & in i2b2 paths, especially in NAACCR tumor registry 
ontology?

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Andrew 
Hangsleben [hangs...@umn.edu]
Sent: Wednesday, October 11, 2017 1:45 PM
To: Russ Waitman
Cc: GPC-DEV@LISTSERV.KUMC.EDU
Subject: Re: SNOW Shrine Hub

Hi Russ,
Looks like I forgot to reload my adapter mappings. I've reloaded them now, but 
I'm having problems running a query with a term that includes an ampersand 
(such as the one you've been testing). I get errors in the proxy.log that 
suggest the ampersand isn't being escaped during some part of the process and 
the query doesn't even make it to shrine. Any thoughts?

Regards,
Andrew

On Wed, Oct 11, 2017 at 10:45 AM, Russ Waitman 
> wrote:
Thanks for sharing Phillip.

Andrew: I see the site seer summary working for a query of just “Breast”!  I 
can then link it to sex=female and a diagnosis icd9 of heart failure!

But, when I add icd-0-3 infiltrating ductal carcinoma (8500/3, 8500/2) as a 
conjunction, it works here and at Dallas but not at UMN.

Russ

From: Phillip Reeder 
Date: Tuesday, October 10, 2017 at 1:36 PM
To: Andrew Hangsleben >, Russ Waitman 
>

Cc: "GPC-DEV@LISTSERV.KUMC.EDU" 
>
Subject: Re: SNOW Shrine Hub

UTSW also had some differences.  I ended up deploying the KUMC as the local 
terminology as well so I could use a 1 to 1 mapping that I got from KUMC and 
added to my existing mapping file.  It does miss some local values that my 
terminology contains, so at some point those may need to be added to the common 
shrine terminology for NAACCR, but it will work for the vast majority of the 
data.

Phillip

From: Gpc-dev 
> 
on behalf of Andrew Hangsleben >
Date: Tuesday, October 10, 2017 at 1:32 PM
To: Russ Waitman >
Cc: "GPC-DEV@LISTSERV.KUMC.EDU" 
>
Subject: Re: SNOW Shrine Hub

Hi Russ,
It looks like our NAACCR ontology was slightly different from yours. Where you 
have:
\\SHRINE_NAACCR\i2b2\naaccr\S:1 Cancer Identification\0521 Morph--Type 
ICD-O-3\850-854\8500/3\
We had:
\\SHRINE_NAACCR\i2b2\naaccr\S:1 Cancer Identification\0521 Morph--Type and 
Behav ICD-O-3\850-854\8500/3\

I replaced our ontology with the one attached to 
https://informatics.gpcnetwork.org/trac/Project/ticket/631. Hopefully we should 
be all set now.

Regards,
Andrew

On Tue, Oct 10, 2017 at 12:02 PM, Russ Waitman 
> wrote:
Hi Kathleen, Andrew and Tim,
We were discussing SHRINE and UMN wrt tumor registry and regular on the dev 
call.

Kathy: to confirm current state:

-  I can run a query for females with heart failure and I hear back 
loud and clear now from UMN!

o   I also hear back from San Antonio, UTSW, KUMC, MCRF (though the count is 
low and I suspect it’s a test database).


-  If I run a query of Breast Cancer and Infiltrating duct carcinoma 
and I get responses from UTSW and KUMC but UMN reports as “could not map query 
terms”.

Russ

From: Gpc-dev 
[mailto:gpc-dev-boun...@listserv.kumc.edu]
 On Behalf Of Andrew Hangsleben
Sent: Monday, October 09, 2017 3:41 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Subject: SNOW Shrine Hub

Hi Everyone,
Could the person responsible for the SNOW hub reach out to me? I think it used 
to be KW, but I'm unsure who it is now.

Regards,
Andrew Hangsleben

--
Andrew Hangsleben
Developer/Analyst
Academic Health Center - Information 
Systems
University of Minnesota
Phone: (612) 625-1285
Email: hangs...@umn.edu



--
Andrew Hangsleben
Developer/Analyst
Academic Health Center - Information 
Systems
University of Minnesota
Phone: (612) 625-1285
Email: hangs...@umn.edu



UT Southwestern


Medical Center



The future of medicine, today.





--
Andrew Hangsleben
Developer/Analyst
Academic Health Center - Information 
Systems
University of Minnesota
Phone: (612) 625-1285
Email: hangs...@umn.edu
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update from Oct 6 PCORNet Data Committee Meeting RE: GPC Dev / Cancer RCR Meeting agenda and meeting notes 10 Oct 2017

[Dan Connolly]

I found...


 *   Draft Agenda Sep 
26<http://listserv.kumc.edu/pipermail/data.pcornet/2017q3/000577.html>

 *   Notes to appear: 
data.pcornet<http://listserv.kumc.edu/pipermail/data.pcornet/> archives

--
Dan

________
From: Dan Connolly
Sent: Tuesday, October 10, 2017 9:12 AM
To: Russ Waitman; gpc-...@listserv.kumc.edu; ,
Subject: RE: GPC Dev / Cancer RCR Meeting agenda and meeting notes 10 Oct 2017

OK... where do we find details on the CDM 4 call for review?

Are notes from the data committee meeting handy?

--
Dan


From: Russ Waitman
Sent: Tuesday, October 10, 2017 9:08 AM
To: Dan Connolly; gpc-...@listserv.kumc.edu; ,
Subject: RE: GPC Dev / Cancer RCR Meeting agenda and meeting notes 10 Oct 2017

Hi Dan,
I might bring up in the context of RCR using the draft MED_ADMIN table and the 
fact that DRNOC is open for CDM 4 draft feedback till the end of the month (Oct 
31st)  I can also give an update from the data committee face to face this past 
Friday if there’s time at the end,

Russ


From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan 
Connolly
Sent: Monday, October 09, 2017 2:38 PM
To: gpc-...@listserv.kumc.edu; ,
Subject: GPC Dev / Cancer RCR Meeting agenda and meeting notes 10 Oct 2017

What else for tomorrow?

  *   shared notes for 10 
Oct<https://docs.google.com/document/d/1dDpw2vV7Zk8Aq3TO56FUDMkYXrB-brEI0w_lKYVPKXM/edit>;
 scribe: MCRF

snapshot:




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

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

b.Roll: Reminder - put institution after your name in GoToMeeting 
preferences

  i.all 12 GPC 
DevTeams<https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams> 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF/MCRI, UMN, UNMC, UTHSCSA, UTSW, 
MU, IU

ii.Today’s meeting is joint with 
the Cancer RCR project

   iii.today's scribe: MCRF

c.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)

   ....none this week...

d.Next Meeting:  24 Oct. scribe: ???

   .17 Oct cancelled due to 
conflict with GPC LEC 16-17 Oct<http://www.gpcnetwork.org/?q=2017LEC>

  i.Note LRU scribe schedule in 
#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:97>

2.
HackathonFive<https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonFive>
 plann Feb 2018

.  Dates for HackathonFive 
survey<https://redcap.kumc.edu/surveys/?s=RY8FAAJ7J3>

3.
Milestone:cancer-rcr-1<https://informatics.gpcnetwork.org/trac/Project/milestone/cancer-rcr-1>
 due 13 Oct
​Cancer RCR Aim 
1<https://docs.google.com/spreadsheets/d/1fY5rR0W4tUEslxjLcXo0J9kDcP2IY7G_i_7mKGr2S9o/edit#gid=1874960144>
 schedule spreadsheet; RCR listserv: 
gpc-rcr<http://listserv.kumc.edu/mailman/listinfo/gpc-rcr>

.  Putting med info in CDM (row 6)
RW: to meet with Keith M. of DRN OC done:
[Gpc-rcr] using Cancer RCR project for testing CDM 4.0 medadmin 
table<http://listserv.kumc.edu/pipermail/gpc-rcr/2017-October/11.html>   
Russ Waitman

a.Site status (Brian G / UIOWA will add details below)

   .UNMC

  i.Indiana University (IU)

ii.Louisiana State University (LSU) 
Health

   iii.Marshfield Clinic: LV

   iv.Medical College of Wisconsin (MCW)

v.Missouri University (MU)

   vi.Medical University of South 
Carolina (MUSC)

  vii.U Florida

viii.UIOWA - Smith

   ix.KUMC - Chandaka / Connolly 
#640<https://informatics.gpcnetwork.org/trac/Project/ticket/640>

x.UMN - McKay

   xi.UTSW

  xii.Vanderbilt

4.
Milestone:grouse-resdac-2<https://informatics.gpcnetwork.org/trac/Project/milestone/grouse-resdac-2>

.  #581 (Crosswalk files for the remaining 4 GPC sites back from GDIT) 
closed<https://informatics.gpcnetwork.org/tra

RE: GPC Dev / Cancer RCR Meeting agenda and meeting notes 10 Oct 2017

[Dan Connolly]

OK... where do we find details on the CDM 4 call for review?

Are notes from the data committee meeting handy?

--
Dan


From: Russ Waitman
Sent: Tuesday, October 10, 2017 9:08 AM
To: Dan Connolly; gpc-...@listserv.kumc.edu; ,
Subject: RE: GPC Dev / Cancer RCR Meeting agenda and meeting notes 10 Oct 2017

Hi Dan,
I might bring up in the context of RCR using the draft MED_ADMIN table and the 
fact that DRNOC is open for CDM 4 draft feedback till the end of the month (Oct 
31st)  I can also give an update from the data committee face to face this past 
Friday if there’s time at the end,

Russ


From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan 
Connolly
Sent: Monday, October 09, 2017 2:38 PM
To: gpc-...@listserv.kumc.edu; ,
Subject: GPC Dev / Cancer RCR Meeting agenda and meeting notes 10 Oct 2017

What else for tomorrow?

  *   shared notes for 10 
Oct<https://docs.google.com/document/d/1dDpw2vV7Zk8Aq3TO56FUDMkYXrB-brEI0w_lKYVPKXM/edit>;
 scribe: MCRF

snapshot:




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

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

b.Roll: Reminder - put institution after your name in GoToMeeting 
preferences

  i.all 12 GPC 
DevTeams<https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams> 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF/MCRI, UMN, UNMC, UTHSCSA, UTSW, 
MU, IU

ii.Today’s meeting is joint with 
the Cancer RCR project

   iii.today's scribe: MCRF

c.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)

   ....none this week...

d.Next Meeting:  24 Oct. scribe: ???

   .17 Oct cancelled due to 
conflict with GPC LEC 16-17 Oct<http://www.gpcnetwork.org/?q=2017LEC>

  i.Note LRU scribe schedule in 
#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:97>

2.
HackathonFive<https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonFive>
 plann Feb 2018

.  Dates for HackathonFive 
survey<https://redcap.kumc.edu/surveys/?s=RY8FAAJ7J3>

3.
Milestone:cancer-rcr-1<https://informatics.gpcnetwork.org/trac/Project/milestone/cancer-rcr-1>
 due 13 Oct
​Cancer RCR Aim 
1<https://docs.google.com/spreadsheets/d/1fY5rR0W4tUEslxjLcXo0J9kDcP2IY7G_i_7mKGr2S9o/edit#gid=1874960144>
 schedule spreadsheet; RCR listserv: 
gpc-rcr<http://listserv.kumc.edu/mailman/listinfo/gpc-rcr>

.  Putting med info in CDM (row 6)
RW: to meet with Keith M. of DRN OC done:
[Gpc-rcr] using Cancer RCR project for testing CDM 4.0 medadmin 
table<http://listserv.kumc.edu/pipermail/gpc-rcr/2017-October/11.html>   
Russ Waitman

a.Site status (Brian G / UIOWA will add details below)

   .UNMC

  i.Indiana University (IU)

ii.Louisiana State University (LSU) 
Health

   iii.Marshfield Clinic: LV

   iv.Medical College of Wisconsin (MCW)

v.Missouri University (MU)

   vi.Medical University of South 
Carolina (MUSC)

  vii.U Florida

viii.UIOWA - Smith

   ix.KUMC - Chandaka / Connolly 
#640<https://informatics.gpcnetwork.org/trac/Project/ticket/640>

x.UMN - McKay

   xi.UTSW

  xii.Vanderbilt

4.
Milestone:grouse-resdac-2<https://informatics.gpcnetwork.org/trac/Project/milestone/grouse-resdac-2>

.  #581 (Crosswalk files for the remaining 4 GPC sites back from GDIT) 
closed<https://informatics.gpcnetwork.org/trac/Project/ticket/581#comment:14> 
fixed

a.#623 (training for GROUSE SQL queries) closed 
fixed<https://informatics.gpcnetwork.org/trac/Project/ticket/623#comment:3>

b.#595 (collect several i2b2 datamarts for GROUSE) closed
<https://informatics.gpcnetwork.org/trac/Project/ticket/595#comment:39>Gold 
stars for getting datamarts in before the LEC: MCW, UNMC, MCRF / MCRI, and UTSW

c.#644 (collect remaining i2b2 datamarts for 

GPC Dev / Cancer RCR Meeting agenda and meeting notes 10 Oct 2017

[Dan Connolly]

What else for tomorrow?

  *   shared notes for 10 
Oct;
 scribe: MCRF

snapshot:




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

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

 *   Roll: Reminder - put institution after your name in GoToMeeting 
preferences

*   all 12 GPC 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF/MCRI, UMN, UNMC, UTHSCSA, UTSW, 
MU, IU

*   Today’s meeting is joint with the Cancer RCR project

*   today's scribe: MCRF

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

*   ...none this week...

 *   Next Meeting:  24 Oct. scribe: ???

*   17 Oct cancelled due to conflict with GPC LEC 16-17 
Oct

*   Note LRU scribe schedule in 
#12

  2.  
HackathonFive
 plann Feb 2018

 *   Dates for HackathonFive 
survey

  3.  
Milestone:cancer-rcr-1
 due 13 Oct
​Cancer RCR Aim 
1
 schedule spreadsheet; RCR listserv: 
gpc-rcr

 *   Putting med info in CDM (row 6)
RW: to meet with Keith M. of DRN OC done:
[Gpc-rcr] using Cancer RCR project for testing CDM 4.0 medadmin 
table   
Russ Waitman

 *   Site status (Brian G / UIOWA will add details below)

*   UNMC

*   Indiana University (IU)

*   Louisiana State University (LSU) Health

*   Marshfield Clinic: LV

*   Medical College of Wisconsin (MCW)

*   Missouri University (MU)

*   Medical University of South Carolina (MUSC)

*   U Florida

*   UIOWA - Smith

*   KUMC - Chandaka / Connolly 
#640

*   UMN - McKay

*   UTSW

*   Vanderbilt

  4.  
Milestone:grouse-resdac-2

 *   #581 (Crosswalk files for the remaining 4 GPC sites back from GDIT) 
closed 
fixed

 *   #623 (training for GROUSE SQL queries) closed 
fixed

 *   #595 (collect several i2b2 datamarts for GROUSE) closed
Gold 
stars for getting datamarts in before the LEC: MCW, UNMC, MCRF / MCRI, and UTSW

 *   #644 (collect remaining i2b2 datamarts for GROUSE) 
created - anybody 
want to race with IU for the next gold star?

  5.  
Milestone:snow-shrine-1,
 
Milestone:snow-shrine-2

 *   #631 
NAACCR Tumor Registry query via GPS SNOW 
SHRINE - UMN too!

*   See also 
NAACCR_ETL,   
#185 (GPC cancer tumor registry ontology) 
reopened

 *   #532 SNOW 
SHRINE node at UNMC with SCILHS PCORnet ontology
News?

 *   #575 SNOW 
SHRINE 1.20.1 install for IU
News?

 *   #411 align 
SNOW SHRINE terminology with SCILHS Ontology
SNOW Shrine 
Ontology   
Andrew Hangsleben: “Out of curiosity, is there any reason we aren't using the 
PCORnet ontology directly in shrine instead of the shrine ontology + adapter 
mappings?
Reeder: “That was a SCHILS decision. Our 

RE: UMN SNOW Tumor Registry

[Dan Connolly]

Fantastic!

verified: UMN NAACCR test@16:52:27

Gold stars all around: I got a plausible count from UMN-AHC for "Demographics + 
Diagnoses@16:56:26" as well.

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Andrew 
Hangsleben [hangs...@umn.edu]
Sent: Thursday, October 05, 2017 3:51 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Subject: UMN SNOW Tumor Registry

Hi Everyone,
UMN cancer cases should now be available on the SNOW shrine network.

Regards,
Andrew

--
Andrew Hangsleben
Developer/Analyst
Academic Health Center - Information 
Systems
University of Minnesota
Phone: (612) 625-1285
Email: hangs...@umn.edu
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RE: SNOW Shrine Ontology

[Dan Connolly]

Yay! Indeed, a simple demographics test gets counts from UMN as well as 
UTHSCSA, MCW, KUMC, and MCRF (but not UTSW? odd...).

As to your question: If I understand correctly, SHRINE adapter mappings are not 
optional. At a minimum, it's a big CSV file with all the terms repeated in both 
the 1st and 2nd column. And the only difference between the PCORNet Ontology 
and our SHRINE ontology is a \SHRINE\ at the beginning. As to why that's 
there... I forget... I think somebody in the ACT network flipped a coin and it 
came up that way, and UTSW followed suit, and we followed from them.

Formally, our decision was made Sep 5... it traces back to a proposal from 
Reeder @ UTSW in the March 22 - Apr 10 timeframe.
https://informatics.gpcnetwork.org/trac/Project/ticket/525#comment:22


--
Dan


From: Andrew Hangsleben [hangs...@umn.edu]
Sent: Tuesday, October 03, 2017 1:18 PM
To: Dan Connolly
Cc: GPC-DEV@LISTSERV.KUMC.EDU
Subject: Re: SNOW Shrine Ontology

Thanks Dan, we should be up and running at UMN now; I ran a few queries to 
verify we were returning results. Out of curiosity, is there any reason we 
aren't using the PCORnet ontology directly in shrine instead of the shrine 
ontology + adapter mappings?

Regards,
Andrew

On Tue, Oct 3, 2017 at 10:54 AM, Dan Connolly 
<dconno...@kumc.edu<mailto:dconno...@kumc.edu>> wrote:
Yes, that's how it works. 
#411<https://informatics.gpcnetwork.org/trac/Project/ticket/411> should have 
details.


--
Dan


From: Gpc-dev 
[gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>] 
on behalf of Andrew Hangsleben [hangs...@umn.edu<mailto:hangs...@umn.edu>]
Sent: Tuesday, October 03, 2017 10:43 AM
To: GPC-DEV@LISTSERV.KUMC.EDU<mailto:GPC-DEV@LISTSERV.KUMC.EDU>
Subject: SNOW Shrine Ontology

Hi Everyone,
We are working on getting our ontology and mappings configured here at UMN. I 
was hoping someone could help me understand which ontologies we are using for 
the SNOW network. My current understanding is that sites are using the 
PCORnet/SCIHLS locally, but we are using the shrine ontology for the network. 
If this is the case, couldn't we just use the SCIHLS ontology for the shrine 
network as well?

Regards,
Andrew Hangsleben

--
Andrew Hangsleben
Developer/Analyst
Academic Health Center - Information 
Systems<http://hub.ahc.umn.edu/ahc-information-systems>
University of Minnesota
Phone: (612) 625-1285<tel:(612)%20625-1285>
Email: hangs...@umn.edu<mailto:hangs...@umn.edu>



--
Andrew Hangsleben
Developer/Analyst
Academic Health Center - Information 
Systems<http://hub.ahc.umn.edu/ahc-information-systems>
University of Minnesota
Phone: (612) 625-1285
Email: hangs...@umn.edu<mailto:hangs...@umn.edu>
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RE: SNOW Shrine Ontology

[Dan Connolly]

Yes, that's how it works. 
#411 should have 
details.


--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Andrew 
Hangsleben [hangs...@umn.edu]
Sent: Tuesday, October 03, 2017 10:43 AM
To: GPC-DEV@LISTSERV.KUMC.EDU
Subject: SNOW Shrine Ontology

Hi Everyone,
We are working on getting our ontology and mappings configured here at UMN. I 
was hoping someone could help me understand which ontologies we are using for 
the SNOW network. My current understanding is that sites are using the 
PCORnet/SCIHLS locally, but we are using the shrine ontology for the network. 
If this is the case, couldn't we just use the SCIHLS ontology for the shrine 
network as well?

Regards,
Andrew Hangsleben

--
Andrew Hangsleben
Developer/Analyst
Academic Health Center - Information 
Systems
University of Minnesota
Phone: (612) 625-1285
Email: hangs...@umn.edu
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GPC SNOW SHRINE status at LEC - 2 Weeks: gold: UTSW, KUMC; silver: MCRF; bronze: WISC, UNMC

[Dan Connolly]

I just ran my weekly demographics + diagnosis site-check query, and the results 
are pretty much the same as last week:

  *   plausible patient count: UTSW, KUMC
  *   counts, but not plausible: MCRF (needs data refresh - 
#531)
  *   could not map query terms: WISC, UNMC 
(#532)
  *   unanticipated problem / unexpected error: MCW, IU 
(#575), UMN 
(#461)
  *   no results (no connectivitiy?): UIOWA 
(#588), CMH 
(#586), UTHSCSA, MU 
(#600)

WISC and UTHSCSA, if you want a ticket about this, we can get you one. :)

I see acknowledgement/updates from UTHSCSA, UIOWA, and CMH (among others) in 
notes from a 27 Sep GPC site PM meeting.

--
Dan

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gpc-dev / Cancer RCR Oct 3 agenda and meeting notes

[Dan Connolly]

Note the featured item:


  1.  
Milestone:cancer-rcr-1
 due 13 Oct

 *   ​Cancer RCR Aim 
1
 schedule spreadsheet, cited from ​28 Sep meeting 
notes

 *   #640 
report completeness of KUMC NAACCR data for Cancer RCR Aim 
1
DC collecting notes 
in 
MolecularTestingStudy


That Aim 1 spreadsheet begins with a bunch of questions from Nick and company:
NAACCR: Verify completeness of required NAACCR data and report status of these 
data

(1) Are data sufficiently fresh, i.e. inclusive of diagnosis years 2013-2016? 
Note that the feasibility showed very low counts for the 2016 diagnosis year 
for a few data partners. (2) Are the following data elements fully populated, 
which are needed to identify single primary solid tumors (primary site [NAACCR 
#400], morphology [NAACCR #521], sequence number [NAACCR # 380 or #560]), 
microscopic confirmation [NAACCR #490]

The rest of the agenda is in progress.

  *   3 Oct gpc-dev shared 
notes
  *   11:00am Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

--
Dan

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ADAPTABLE Query 3

[Dan Connolly]

FYI...


From: Riley, Danielle [danielle-ri...@uiowa.edu]
Sent: Monday, September 25, 2017 10:40 AM
To: Dan Connolly
Subject: DEV call agenda items for 9/26/17


Hi Dan,


Below are ADAPTABLE updates that I think the DEV team members would be 
interested in knowing. Can you add them to the agenda for tomorrow's call?


  1.  Query 3 Schedule
 *   Release Date: October 30th
 *   Results Due: November 13th
  2.  Query 3 Updates
 *   Will be adding smoking history
 *   Addition of medical history, lab results, and medications has been 
postponed until Query 4


Thanks!


Danielle J. Riley

PhD Candidate
Department of Epidemiology
College of Public Health, University of Iowa
danielle-ri...@uiowa.edu

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gpc-dev 26 Sep agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 26 Sep shared 
notes;
 scribe: WISC

current snapshot:



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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: WISC

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

 *   Next Meeting:  3 Oct. scribe: MCRF?

*   Note LRU scribe schedule in 
#12

  2.  PCORnet Data Committee Monthly Meeting..Note social determinants survey 
   Russ Waitman

  3.  
Milestone:cohort-char1

 *   #639 MCW 
Height/Wt data only covers survey 
respondents - KK? 
GK?

 *   #379 Link 
EHR data to Health and Medical Research Family Survey (HMRFS) 2 
results

*   Suarez, IRB news?

*   Bokov, talked with Debbie about WISC data?

  4.  
Milestone:snow-shrine-1

 *   #532 SNOW 
SHRINE node at UNMC with SCILHS PCORnet ontology
UNMC Prod Spoke 
"site check 25 Sep@10:17:09" - Could not map query term(s).

 *   #575 SNOW 
SHRINE 1.20.1 install for 
IU:
19 Sep: “Hopefully in a day or two.”
IU SPOKE PROD "site check 25 Sep@10:17:09"- An unanticipated problem 
encountered.

  5.  Milestone:snow-shrine-2
#280
 Medication ontology orgainzed by ingredient
Med ontology 
missing NDC 
question   Russ 
Waitman

  6.  Milestone:grouse-resdac-2
Ticket
 #593 (Please load the MCW terms file into Babel) 
closed 
fixed (right?)

  7.  FW: GPC c003, Initial Refresh Feedback 
   Russ Waitman

 *   CMH

 *   MCRF

 *   MCW

 *   IU

 *   UIOWA

 *   KUMC: not aware of any plans to diagnose 20 diagnoses per inpatient 
encounter (Connolly 21 
Sep)

 *   UMN

 *   MU

 *   UNMC: “Our deployment is in compliance with the CDMV31 specifications 
and I do not expect to change until such time that the CDMV31 spec is revised.” 
(JRC 22 Sep)

 *   UTHSCSA

 *   UTSW

 *   WISC - too late for Oct 16 (DY 21 
Sep)

  8.  
Milestone:next-d

 *   #571 
characterization of data from next-d GPC 
sites re-opened; 
requested by 29 Sep:

*   your site's CDM Cycle 3 Refresh 1 EDC report  to 
https://redcap.gpcnetwork.org/surveys/?s=9LT4KE8NFD

*   how your site will be representing Observation Stays for CDM Cycle 
3 Refresh 2 (C3R2) coming up in October

 *   #545 Study 
sample and DM sample definition for 
next-d

*   IU: done 20 Sep

*   NextD - Ticket 545 Inquiry for 
UNMC   Gardner, 
Bret J
all set? Replies from Liu, Stoddard suffice?

*   MU

*   UMN

  9.  Milestone:gpc-phase2-h5

RE: GPC c003, Initial Refresh Feedback

[Dan Connolly]

At the risk of getting an anybody/somebody/nobody response, I'm going to use 
one message for the rest of these:

Each site please respond with an estimate of whether you'll get this addressed 
in the Oct 16 refresh:

IU: ICD9 past Oct 15

UIOWA: Encounter date skew, UN encounters, Procedures stuff, Vitals down by 26%

KUMC: More than 20 diagnoses per inpatient encounter. It would take around half 
a day to diagnose it. If the diagnosis says the fix is easy, then perhaps we 
could address this for the Oct 16. But I'm not aware of any plans to even try 
to diagnose it.

UMN: lots of principal diagnoses per EI

MU: DEATH down by 85%

UNMC: 33% of PX are NDC; move to DISPENSING? (er... I'm pretty sure gpc-dev 
asked and were advised to put them in PX. IOU a link)

UTHSCSA: lab_name vs loinc for Troponin, CK MB

UTSW: 20% UN encounters

WISC: 5.7 principal DX / EI; lab loinc stuff



--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Russ Waitman 
[rwait...@kumc.edu]
Sent: Thursday, September 21, 2017 1:13 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Cc: Darcy Louzao, Ph.D.; Lesley Curtis; Laura Qualls
Subject: FW: GPC c003, Initial Refresh Feedback

Hi DRNOC,
Thanks for sharing.  I think it may be a short turn around to get much fixed in 
less than a month but sharing to see what’s possible.

Hi GPC Dev,
Just got info on further EDC analysis from Duke.

Dan: can we queue up for a GPC-DEV call in the future?

Russ

From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Thursday, September 21, 2017 12:19 PM
To: Russ Waitman
Cc: Lesley Curtis; Darcy Louzao, Ph.D.; Laura Qualls
Subject: GPC c003, Initial Refresh Feedback

Good afternoon,

As part of our recent Data Curation Review Process, we spent time reviewing the 
data across numerous areas. This was not meant to be an in-depth review of 
every single DataMart, but in some cases, we found items which were either not 
part of the EDC report or part of the EDC report but not fully reported.  While 
not comprehensive, the attached supplemental items were flagged for DataMarts 
in your CDRN and could benefit from investigation. We recommend investigating 
these items to determine if they are remediable or an accurate reflection of 
source data.  If an item is remediable, please address it as soon as possible. 
If it is not feasible to incorporate changes in the upcoming refresh (due 
October 16th), items may be remediated in an off-cycle refresh or in Cycle 4 
(January 2018). If you have any questions or comments regarding these 
observations or would like to request an off-cycle refresh please contact us at 
dr...@pcornet.org.

Thanks,
The Data Curation Team
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MCW: NI Encounters, Procedures per IP RE: GPC c003, Initial Refresh Feedback

[Dan Connolly]

Brad, are you likely to get these addressed by the Oct 16 refresh?

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Russ Waitman 
[rwait...@kumc.edu]
Sent: Thursday, September 21, 2017 1:13 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Cc: Darcy Louzao, Ph.D.; Lesley Curtis; Laura Qualls
Subject: FW: GPC c003, Initial Refresh Feedback

Hi DRNOC,
Thanks for sharing.  I think it may be a short turn around to get much fixed in 
less than a month but sharing to see what’s possible.

Hi GPC Dev,
Just got info on further EDC analysis from Duke.

Dan: can we queue up for a GPC-DEV call in the future?

Russ

From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Thursday, September 21, 2017 12:19 PM
To: Russ Waitman
Cc: Lesley Curtis; Darcy Louzao, Ph.D.; Laura Qualls
Subject: GPC c003, Initial Refresh Feedback

Good afternoon,

As part of our recent Data Curation Review Process, we spent time reviewing the 
data across numerous areas. This was not meant to be an in-depth review of 
every single DataMart, but in some cases, we found items which were either not 
part of the EDC report or part of the EDC report but not fully reported.  While 
not comprehensive, the attached supplemental items were flagged for DataMarts 
in your CDRN and could benefit from investigation. We recommend investigating 
these items to determine if they are remediable or an accurate reflection of 
source data.  If an item is remediable, please address it as soon as possible. 
If it is not feasible to incorporate changes in the upcoming refresh (due 
October 16th), items may be remediated in an off-cycle refresh or in Cycle 4 
(January 2018). If you have any questions or comments regarding these 
observations or would like to request an off-cycle refresh please contact us at 
dr...@pcornet.org.

Thanks,
The Data Curation Team
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MCRF IC encounters, INR labs RE: GPC c003, Initial Refresh Feedback

[Dan Connolly]

Laurel, Marshfield folks, what are the odds you can get these addressed by the 
Oct 16 refresh?

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Russ Waitman 
[rwait...@kumc.edu]
Sent: Thursday, September 21, 2017 1:13 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Cc: Darcy Louzao, Ph.D.; Lesley Curtis; Laura Qualls
Subject: FW: GPC c003, Initial Refresh Feedback

Hi DRNOC,
Thanks for sharing.  I think it may be a short turn around to get much fixed in 
less than a month but sharing to see what’s possible.

Hi GPC Dev,
Just got info on further EDC analysis from Duke.

Dan: can we queue up for a GPC-DEV call in the future?

Russ

From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Thursday, September 21, 2017 12:19 PM
To: Russ Waitman
Cc: Lesley Curtis; Darcy Louzao, Ph.D.; Laura Qualls
Subject: GPC c003, Initial Refresh Feedback

Good afternoon,

As part of our recent Data Curation Review Process, we spent time reviewing the 
data across numerous areas. This was not meant to be an in-depth review of 
every single DataMart, but in some cases, we found items which were either not 
part of the EDC report or part of the EDC report but not fully reported.  While 
not comprehensive, the attached supplemental items were flagged for DataMarts 
in your CDRN and could benefit from investigation. We recommend investigating 
these items to determine if they are remediable or an accurate reflection of 
source data.  If an item is remediable, please address it as soon as possible. 
If it is not feasible to incorporate changes in the upcoming refresh (due 
October 16th), items may be remediated in an off-cycle refresh or in Cycle 4 
(January 2018). If you have any questions or comments regarding these 
observations or would like to request an off-cycle refresh please contact us at 
dr...@pcornet.org.

Thanks,
The Data Curation Team
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CMH: ICD9/10, vital outliers RE: GPC c003, Initial Refresh Feedback

[Dan Connolly]

OK, but as usual, let's start the discussion in writing and follow up on the 
call if that's not sufficient.

CMH folks, what are the odds you can get CMH: ICD9/10, vital outliers addressed 
in the October 16th refresh?

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Russ Waitman 
[rwait...@kumc.edu]
Sent: Thursday, September 21, 2017 1:13 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Cc: Darcy Louzao, Ph.D.; Lesley Curtis; Laura Qualls
Subject: FW: GPC c003, Initial Refresh Feedback

Hi DRNOC,
Thanks for sharing.  I think it may be a short turn around to get much fixed in 
less than a month but sharing to see what’s possible.

Hi GPC Dev,
Just got info on further EDC analysis from Duke.

Dan: can we queue up for a GPC-DEV call in the future?

Russ

From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Thursday, September 21, 2017 12:19 PM
To: Russ Waitman
Cc: Lesley Curtis; Darcy Louzao, Ph.D.; Laura Qualls
Subject: GPC c003, Initial Refresh Feedback

Good afternoon,

As part of our recent Data Curation Review Process, we spent time reviewing the 
data across numerous areas. This was not meant to be an in-depth review of 
every single DataMart, but in some cases, we found items which were either not 
part of the EDC report or part of the EDC report but not fully reported.  While 
not comprehensive, the attached supplemental items were flagged for DataMarts 
in your CDRN and could benefit from investigation. We recommend investigating 
these items to determine if they are remediable or an accurate reflection of 
source data.  If an item is remediable, please address it as soon as possible. 
If it is not feasible to incorporate changes in the upcoming refresh (due 
October 16th), items may be remediated in an off-cycle refresh or in Cycle 4 
(January 2018). If you have any questions or comments regarding these 
observations or would like to request an off-cycle refresh please contact us at 
dr...@pcornet.org.

Thanks,
The Data Curation Team
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gpc-dev 19 Sep agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 19 Sep shared 
notes;
 scribe: UTSW




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UTSW

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

*   None this week

 *   Next Meeting:  19 Sep. scribe?

*   Note LRU scribe schedule in 
#12

  2.  
Milestone:cohort-char1
 25 Sep

 *   #570 
collect expanded obesity cohort data: demographics, income, insurance / 
financial class
ref : Minutes from 
Height/Weight Cohort Call for 
9/13/17

*   UIOWA - technical staff assigned to submit data. 
(#570 owner: BG)

   *   does "13 Sep: Should be done before the end of next week" apply 
here? I didn't confirm with Alex.

*   MCW - submitted demographics; but only for survey respondents 
(#639 owner:GK)

*   WISC: Alex notes some patient mapping issue; plans to double-check 
and follow up on 
comment:41.
 (#570 owner: AB)

*   UTSW - regulatory conversation with children's hospital in progress
"Olivia will be contacting the IRB or the PI on this issue” (#570)

  3.  
Milestone:snow-shrine-1,

 *   #532 SNOW 
SHRINE node at UNMC with SCILHS PCORnet 
ontology

 *   #575 SNOW 
SHRINE 1.20.1 install for 
IU

  4.  Milestone:snow-shrine-2

 *   #636 (MU incoming SHRINE traffic getting blocked on port 6443) 
closed 
fixed

 *   #634 (MCRF needs DNS entry for SNOW SHRINE prod spoke server) 
closed 
fixed

  5.  
Milestone:next-d
 23 Oct
#545 - table 1 subset: status updates?

 *   UNMC - ETA was: week of 15 Sep

 *   MU - ETA was: week of 22 Sep at the earliest

 *   IU - was: pending IU approval of limited dataset DUA

 *   UMN - ETA was: UMN DROC approval + 1 week

  6.  
Milestone:gpc-phase2-h5

 *   #431 
Deploy free text notes and de-identification at majority of GPC sites 
(milestone 2.12.1)
KUMC + MCW + … 
volunteers? nominations?

*   MCRF -  George - to help find standalone package details

*   UNMC - to follow-up with those who can speak to resource allocation

*   IU - will ask Bill Barnett (site PI)

 *   #573 
de-identified text notes for on a cohort-by-cohort basis
Kris at MCW to 
generate spreadsheet of 5-20 popular note types, how they are mapped at their 
site, and general descriptions to guide mapping at other sites.

  7.  PCORI Molecular Testing Rapid Cycle Research proposal of 8 Aug is funded

 *   Brian G / UIOWA to share details after meeting with Betsy and others



--
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gpc-dev 12 Sep agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 12 Sep shared 
notes;
 scribe: UMN




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU , 
IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UMN

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

*   #63 (shared ICD9CM diagnosis term hierarchy) re-opened; 
closed 
per 
ticket:411#comment:2

*   #67 (Demographics ontology and value sets, e.g. age) re-opened; 
closed

 *   Next Meeting:  19 Sep. scribe: ???

*   Note LRU scribe schedule in 
#12

*   #431 
Deploy free text notes and de-identification at majority of GPC sites 
(milestone 2.12.1) 
- for next week?

  2.  
Milestone:cohort-char1
 18 Sep

 *   #570 
collect expanded obesity cohort data: demographics, income, insurance / 
financial class
8 Aug: UIOWA asked 
if data less geocodes is interesting
14 Aug: UTHSCSA says yes
News? On track for 18 Sep? Better ETA?

  3.  
Milestone:snow-shrine-1,

 *   #602 SNOW 
SHRINE authorization and governance
Last week:

*   Cow logo 

 added to ticket #602

*   “Ticket will be closed once the process is communicated to the rest 
of the GPC.”

 *   #532 SNOW 
SHRINE node at UNMC with SCILHS PCORnet 
ontology moved to 
shrine-1 milestone based on 5 Sep comment:10

 *   #613 IU 
update spoke(s) with prod hub 
cert news?

  4.  Milestone: 
snow-shrine-2

 *   #411 align 
SNOW SHRINE terminology with SCILHS 
Ontology

*   #186 (Querying age by numerical constraints) re-opened; closed 
wontfix 
- not in our SHRINE ontology

*   Re-opened to confirm SHRINE interop:

   *   #23 (how to query for BMI and other core clinical measurements?) 
reopened

   *   #120 (encounter terms; e.g. discharge disposition, encounter 
type, provider) 
reopened

   *   #243 (GPC Procedure Ontology: CPT, HCPCS) 
reopened

   *   #229 (Enrollment terms based on Catchment Area, encounters, 
etc.) 
reopened

  5.  
Milestone:grouse-resdac-2

 *   #595 
collect i2b2 datamarts for 
GROUSE

*   UNMC done. Yay!

*   Who’s next?

 *   #623 
training for GROUSE SQL 
queries GPC pilots 
13, 26...




--
Dan

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gpc-dev 29 Aug agenda and meeting notes (in progress)

[Dan Connolly]

What else for tomorrow?

Please excuse the delay in collecting the agenda into one place; it's something 
of a skeleton so far...

  *   gpc-dev 29 Aug shared 
notes;
 scribe: KUMC




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: KUMC

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

*
 *   Next Meeting:  @@. scribe: ??

*   Note LRU scribe schedule in 
#12

  2.  stuff from last week 
(#12)

  3.  stuff from tickets by 
milestone

  4.  Milestone:Next-d Sep 5?
#545: “Short notice 
data request for GPC sites to extract data on a subset of Table 1 without the 
'DM onset date' column and return the results to Northwestern by 9/5.”

  5.  stuff from gpc-dev 
email

  6.  new/closed/reopened 
tickets



--
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gpc-dev 22 Aug meeting notes

[Dan Connolly]

Please do join us today at 11. ​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

Agenda is in progress; please excuse the delay...

  *   gpc-dev 22 Aug shared 
notes;
 scribe: IU

--
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RE: gpc-dev 15 Aug agenda and meeting notes

[Dan Connolly]

Gotomeeting is on the fritz. George is unavailable. The meeting is canceled.

The people noted as owners of the shrine issues, please hit the "accept" button 
or otherwise acknowledge that you own them.

--
Dan

____
From: Dan Connolly
Sent: Monday, August 14, 2017 2:30 PM
To: ,
Cc: Al'ona Furmanchuk
Subject: gpc-dev 15 Aug agenda and meeting notes

What else for tomorrow?

  *   gpc-dev 15 Aug shared 
notes<https://docs.google.com/document/d/1O1ZBH77yeabmexpI1tIiReI5V_GdXWrfS-77ixnmpU4/edit>;
 scribe: WISC




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

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

 *   roll: all 12 
DevTeams<https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams> 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: WISC

 *   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)

*   #630 (KUMC shrine.keystore broken on prod spoke server and SNOW 
SHRINE test hub) 
created<https://informatics.gpcnetwork.org/trac/Project/ticket/630> minor

*   #614 (UTHSCSA update spoke(s) with prod hub cert) 
closed<https://informatics.gpcnetwork.org/trac/Project/ticket/614#comment:7> 
fixed 10 Aug

*   #605 (UMN update spoke(s) with prod hub cert) 
closed<https://informatics.gpcnetwork.org/trac/Project/ticket/605#comment:10> 
fixed

*   #612 (UNMC update spoke(s) with prod hub cert) 
closed<https://informatics.gpcnetwork.org/trac/Project/ticket/612#comment:4> 
fixed

*   #290 (integrate interim report enrollment data collection with 
quarterly QA ...) 
closed<https://informatics.gpcnetwork.org/trac/Project/ticket/290#comment:20> 
invalid

 *   Next Meeting:  22 Aug. scribe?

*   Note LRU scribe schedule in 
#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:97>

  2.  Milestone:grouse-resdac-2
<https://informatics.gpcnetwork.org/trac/Project/milestone/grouse-resdac-2>#621<https://informatics.gpcnetwork.org/trac/Project/ticket/621>
 review GPC Pilot 
applications<https://informatics.gpcnetwork.org/trac/Project/ticket/621> 
reminder (see mail from Steve Fennel August 14, 2017 11:25 AM)

  3.  Milestone:next-d
#546<https://informatics.gpcnetwork.org/trac/Project/ticket/546> next-d code - 
GK, how is it going?

  4.  Milestone:shrine-2

 *   #613 (IU update spoke(s) with prod hub cert) 
reopened<https://informatics.gpcnetwork.org/trac/Project/ticket/613#comment:6> 
assigned to Tony F, right?

 *   #624 (KUMC i2b2 lacks fine-grain age for young children) 
created<https://informatics.gpcnetwork.org/trac/Project/ticket/624>; minor, 
right Russ?

 *   #625 (Disk space allocation and LVM setup for SNOW SHRINE spoke 
server(s)) created<https://informatics.gpcnetwork.org/trac/Project/ticket/625> 
Keith is working on it.

 *   #626 (UTHSCSA needs static IP address for SHRINE) 
created<https://informatics.gpcnetwork.org/trac/Project/ticket/626> Hough, 
assigned to you, right?

 *   #628 (UIOWA network traffic still being blocked for prod spoke) 
created<https://informatics.gpcnetwork.org/trac/Project/ticket/628>; Nick, 
assigned to you, right?

 *   #629 (KUMC network connectivity issue - test spoke to SNOW SHRINE test 
hub) created<https://informatics.gpcnetwork.org/trac/Project/ticket/629>; Lav, 
assigned to you, right?

 *   #631 (NAACCR Tumor Registry query via GPS SNOW SHRINE) 
created<https://informatics.gpcnetwork.org/trac/Project/ticket/631>; Lav is 
working on it




--
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gpc-dev 15 Aug agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 15 Aug shared 
notes;
 scribe: WISC




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: WISC

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

*   #630 (KUMC shrine.keystore broken on prod spoke server and SNOW 
SHRINE test hub) 
created minor

*   #614 (UTHSCSA update spoke(s) with prod hub cert) 
closed 
fixed 10 Aug

*   #605 (UMN update spoke(s) with prod hub cert) 
closed 
fixed

*   #612 (UNMC update spoke(s) with prod hub cert) 
closed 
fixed

*   #290 (integrate interim report enrollment data collection with 
quarterly QA ...) 
closed 
invalid

 *   Next Meeting:  22 Aug. scribe?

*   Note LRU scribe schedule in 
#12

  2.  Milestone:grouse-resdac-2
#621
 review GPC Pilot 
applications 
reminder (see mail from Steve Fennel August 14, 2017 11:25 AM)

  3.  Milestone:next-d
#546 next-d code - 
GK, how is it going?

  4.  Milestone:shrine-2

 *   #613 (IU update spoke(s) with prod hub cert) 
reopened 
assigned to Tony F, right?

 *   #624 (KUMC i2b2 lacks fine-grain age for young children) 
created; minor, 
right Russ?

 *   #625 (Disk space allocation and LVM setup for SNOW SHRINE spoke 
server(s)) created 
Keith is working on it.

 *   #626 (UTHSCSA needs static IP address for SHRINE) 
created Hough, 
assigned to you, right?

 *   #628 (UIOWA network traffic still being blocked for prod spoke) 
created; Nick, 
assigned to you, right?

 *   #629 (KUMC network connectivity issue - test spoke to SNOW SHRINE test 
hub) created; Lav, 
assigned to you, right?

 *   #631 (NAACCR Tumor Registry query via GPS SNOW SHRINE) 
created; Lav is 
working on it




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gpc-dev 8 Aug agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 8 Aug shared 
notes;
 scribe: scribe: MCRF? (offer to scribe last week still good this week?)




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: MCRF? (offer to scribe last week still good this 
week?)

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

*   #544 
how to convert ACS raw variables to CAP variables (e.g. type of health 
insurance)? Closed 
fixed

*   #290 (integrate interim report enrollment data collection with 
quarterly QA ...) 
closed 
invalid

 *   Next Meeting:  15 Aug. scribe: WISC? KUMC?

*   Note LRU scribe schedule in 
#12

*   GK to walk thru 
#546 next-d code? 
Too soon? KUMC loses its summer student ~20 Aug. Other alpha/beta test site?

  2.  Milestone:cohort-char1
#570
 collect expanded obesity cohort data: demographics, income, insurance / 
financial class
Update on geocoding 
IRB issue from UIOWA?

  3.  
Milestone:cdm-cycle3
 reflection

 *   #579 (Data Characterization - Cycle 3 Tracking) 
closed 
(yay!)

 *   Review KUMC EDC report.

 *   EDC reports / issues from other sites?

  4.  
Milestone:grouse-resdac-2

 *   #595 
collect i2b2 datamarts for GROUSE
Thanks, UTSW (along 
with MCW, MCRF, UIOWA).
UNMC is nominated to go next, in order to facilitate the rapid cycle research 
project

 *   #621 
review GPC Pilot 
applications - 
having fun? Anyone at risk for 17 Aug?

 *   #623 
training for GROUSE SQL 
queries - 
brainstorm a bit?



--
Dan

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how KUMC loads the SSDMF files

[Dan Connolly]

The bulk of the work is done in 
ssdmf_load.sql.
 It matches on SSN and birth date and adds info to patient_mapping, 
encounter_mapping, patient_dimension, and observation_fact.


The table schema we use is in 
ssdmf_table.sql:

create table ssdmf_table ("ADD_CHANGE_DELETE" varchar2(1)
, "SOCIAL_SECURITY_NUMBER" varchar2(9)
, "LAST_NAME" varchar2(20)
, "NAME_SUFFIX" varchar2(4)
, "FIRST_NAME" varchar2(15)
, "MIDDLE_NAME" varchar2(15)
, "VERIFY_OR_PROOF_CODE" varchar2(1)
, "DATE_OF_DEATH" date
, "DATE_OF_BIRTH" date
, "STATE_COUNTRY_CODE_OF" varchar2(2)
, "ZIP_CODE_LAST_RESIDENCE" varchar2(5)
, "ZIP_CODE_LUMP_SUM_PAYMENT" varchar2(5))

NTIS publishes regular deltas rather than the whole database. We use 
get_updates.py
 to download the deltas and 
dmf_monthly_etl.sql
 to apply them. (These are both wrapped in Jenkins jobs.)

--
Dan

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gpc-dev 1 Aug: cancel in 3... 2... 1...

[Dan Connolly]

I haven't managed to get an agenda together. Is there anything sufficiently 
important to discuss today that I shouldn't cancel?


--
Dan

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gpc-dev 25 July agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 25 July shared 
notes;
 scribe: UTSW




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UTSW

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

*   #593 
MCW terms on Babel 
promoted to major
(tracking MCRF, CMH in this ticket too, for now)

*   #596 (targeted cancer therapy study - Query 1, 2, 3) 
closed 
fixed

*   #611 (MCW update spoke with prod hub cert) 
closed 
fixed

 *   Next Meeting:  1 Aug. scribe: ??

*   Note LRU scribe schedule in 
#12

  2.  
Milestone:cdm-cycle3
 due July 31

 *   #579 Data 
Characterization - Cycle 3 
Tracking

*   Approved: UNMC, MCW, WISC, KUMC

*   CMH - ?

*   others?

  3.  
Milestone:next-d

 *   #544 how 
to convert ACS raw variables to CAP variables (e.g. type of health insurance)?
Code for approach 
2: 
LinkEHRAndGeocodedData.sql
 4ba0ac2

  4.  #377 Social Security Death Master file
“Does 
anyone have a current data dictionary for these files?”

  5.  Review of current work by owner 
site




--
Dan

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RE: unable to connect to babel webclient

[Dan Connolly]

Try again?

It didn't reboot cleanly after some regular maintenance. Lav address the issue. 
I can log in now.

--
Dan


From: Mosa, Abu S. [mo...@health.missouri.edu]
Sent: Thursday, July 20, 2017 11:49 AM
To: Dan Connolly
Cc: <gpc-dev@listserv.kumc.edu>; Mandhadi, Vasanthi (Medical Research Office)
Subject: RE: unable to connect to babel webclient

Hi Dan,

I am getting the below error when I try to login to GPC babel. I need to look 
into the adaptable query that was created by Sravani. Thanks.

Regards,
Dr. Abu Saleh Mohammad Mosa, MS, PhD
Director, Research Informatics
University of Missouri School of Medicine
Assistant Research Professor of Health Informatics
Health Management and Informatics
One Hospital Drive, NW505, DC018.00
Columbia, MO 65212
Phone: 573-882-8349
Email: mo...@health.missouri.edu<mailto:mo...@health.missouri.edu>
Web: medicine.missouri.edu | hmi.missouri.edu

From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Mosa, Abu 
S.
Sent: Tuesday, July 18, 2017 4:02 PM
To: <gpc-dev@listserv.kumc.edu> <gpc-dev@listserv.kumc.edu>
Subject: unable to connect to babel webclient

Hi,

I am unable to connect to babel webclient. Here is the error:

[cid:image001.png@01D3014E.41135820]

Regards,
Mosa
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RE: facility_id mapping for Next-D (#539)

[Dan Connolly]

Prof. Black, Alona,

This facility_id mapping... what will it map from? What sort of info should we 
add to encounter.facility_id (or elsewhere in the CDM... or elsewhere 
altogether?) as input to this mapping?

Feel free to answer at your convenience. It'll be weeks or months before we 
make the relevant changes to our CDM ETL, so there's no particular rush.

--
Dan



From: furmanc...@icnanotox.org [furmanc...@icnanotox.org] on behalf of Al'ona 
Furmanchuk [alona.furmanc...@northwestern.edu]
Sent: Thursday, May 18, 2017 11:16 AM
To: gpc-dev@listserv.kumc.edu
Cc: Dan Connolly; Mei Liu; a...@nm.org; nicholas-c-sm...@uiowa.edu; 
phillip.ree...@utsouthwestern.edu; Lindsey Lynne Cook; Russ Waitman; 
brian-gryz...@uiowa.edu; George Kowalski; meye0...@umn.edu; 
jay.peder...@unmc.edu; danh...@regenstrief.org; adfre...@regenstrief.org; 
mcneele...@health.missouri.edu; Brennan Connolly
Subject: Re: [gpc-informatics] #539: Next-D Clinical Variables in EMR: how to 
collect?

Thank you for fast follow up on this. See below my comments that hopefully 
might help:

On 3:
NWM system provides facility_id number in CDM which is could be used just to 
distinguish between different facilities. During the meeting it was decided 
that better characterization (beyond PCORNET CDM) of facility should be done. 
Prof. Black will provide proper mapping on this.

On 9:
It was in distributed for the in-person meeting materials (attaching relevant 
file here as well). I added two extra columns specifying what variable from 
what PCORNET CDM tables should be used for each data element of CMS 
measurement. I also provided corresponding analogues values in case if theirs 
standards codings are varied from PCORNET ones.

Thank you.
Alona.

On Thu, May 18, 2017 at 10:27 AM, GPC Informatics 
<d...@madmode.com<mailto:d...@madmode.com>> wrote:
#539: Next-D Clinical Variables in EMR: how to collect?
--+---
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  design-issue  |  Status:  assigned
 Priority:  minor |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  542
 Blocking:|
--+---
Changes (by meiliu):

 * cc: lindsey.cook@… (removed)
 * cc: cgladfelter, bconnolly@… (added)
 * owner:  afurmanchuk => meiliu


Comment:

 reviewing May 16 in-person meeting version of //Proposed Formats for Data
 Extraction// with Dan and Brennan:

 by table:
  1. summary information is relatively clear; see #545
  2. demographics seems like a straightforward extract from CDM
- date structure (year-month, days since 1st encounter) is novel but
 workable
  3. **CDM encounter.facility_id is all "no information" NI at KUMC**
  4. meds - all CDM columns OK
 - Dan recalls seeing requirements for all these columns in the EDC
 report
  5. vitals - smoking seems to be OK at KUMC
  6. labs is a little tricky, but see #551
 a. from CDM short-list
 b. Glucose etc.
  7. non-urgent visits
 - some variability among GPC sites was noted regarding what counts as
 `enc_type=AV`
 - codes are in table B1; e.g. 993385 New Patient, Adult
  8. immunization
 - draws from CDM PROCEDURES table; eg px_type=C3/C4/CH pc=90732 for
 Pneumococcal conjucate vaccine
  9. Health outcomes: Glycemic control, LDL control, Pneumococcal
 vaccinations
 - this table is less well-defined: no sketch of which CDM tables /
 columns are relevant
 - much material draws from CMS122v5
  10. diagnosis
 - note: CDM DIAGNOSIS is only billing diagnoses; problem list
 diagnoses go in the CONDITION table, which was not characterized in
 milestone:cdm-c2r2


 Mei to follow up on options regarding missing `facility_id` data.

--
Ticket URL: 
<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_trac_Project_ticket_539-23comment-3A9=DwIDaQ=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=-aRkmw3Ob1oZRrrYmR1wHysw9FWMRlmk_CMIVWKi32KhS_EbXW7cMBGcBAmqh95W=s1Kzf1392oP6F3gs6uqK2scaV9R3WbcrypgMOf8Lx10=uVWtTRnqaZbOOebENIN3dHG5jYXbhSLuD5xG1OiO5V0=
 >
gpc-informatics 
<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_=DwIDaQ=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=-aRkmw3Ob1oZRrrYmR1wHysw9FWMRlmk_CMIVWKi32KhS_EbXW7cMBGcBAmqh95W=s1Kzf1392oP6F3gs6uqK2scaV9R3WbcrypgMOf8Lx10=B1mVEpFHig575645iWM5OD3tKEzXgwfj8a34J__yHpk=
 >
Greater Plains Network - Informatics



--
Al’ona Furmanchuk, Ph.D.
Research Associate

Department of Electrical Engineering and Computer Science
Northwestern University
2145 Sheridan Road, Tech L359
Evanston, IL 60208
Web: http://furmanchuk.com/
E-mail: alona.furmanc...@northwestern.edu<mailto:furmanc...@icnanotox.org>
Phone: 847-467-2299
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gpc-dev 18 Jul agenda and meeting notes (incl. next-d geocoding #544)

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 18 July shared 
notes;
 scribe: UMN




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UMN

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

*   #622 
PCORNet CDM Cycle 2 Refresh 2 experience report - 
CMH

 *   Next Meeting:  25 July. scribe: ???

*   Note LRU scribe schedule in 
#12

  2.  #478 (ADAPTABLE monitoring) 
reopened:
 “Query 2 will be distributed to all the sites on 08/07/2017. We(KUMC) offered 
to be a beta tester site for the Query 2. Query was shared with KUMC on 
07/14/2017. Maren Wennberg from KUMC will be working on it.”

  3.  #596 targeted 
cancer therapy study feasibility 
queries due 18 July

 *   Nicholas: will submit UIOWA’s data on query 3 and send an update out 
to the group. Done:
DROC Breast Cancer CRG Request 
(#596)   Smith, 
Nicholas C

 *   Re - in LOINC: Nick to make an adjustment for Query 3 on site specific 
factor 15  and repair the LOINC issue.

 *   Jim: Will put revised query 3 on the ticket. (OBE?)

 *   Query 1, 2, 3:

*   UNMC - “I am forwarding all three data queries to Nick.” - Campbell 
Fri 12:47:47
“Thanks for forwarding it, Jim” Smith Fri 12:51 PM

*   MCRF - “I submitted results from Marshfield based on ...” Verhagen 
Thu Jul 13 17:17:02
“No this [missing LOINC] is not a problem.” -Smith Fri 11:34:15

*   UTSW - “Query 1,2,& 3 have been uploaded by UTSW.” -- Reeder Mon 
13:03:29

*   MU: “if that [replaced 560 with 380] works then there is no need 
for me to re-run them, cause that is the data you have” - McNeely Fri 13:42:55

*   WISC -

*   KUMC -

*   MCW -

*   UMN -

  4.  
Milestone:cdm-cycle3
 due July 31

 *   #549 (discharge info disconnected from parts of some EI visits) closed 
fixed

 *   #589 
principal diagnosis 10% threshold in PCORNet 
CDM news from IU?

 *   #579 Data 
Characterization - Cycle 3 
Tracking

  5.  Milestone:cohort-char1
#570: 
collect expanded obesity cohort data 
comment:43:

 *   MCW done July 14 (comment:47)

 *   UIOWA ETA? Brian will talk this through with Mike Bingham on 7/25

  6.  Milestone:gpc-phase2-h4
#408
 collect Enrollment numbers for interim report (milestone 
2.3.5) in progress

  7.  
Milestone:next-d

 *   #544 how 
to convert ACS raw variables to CAP variables (e.g. type of health insurance)?
Attachment 
GeocodingOptionsForGPC-2017_06_27-bb.docx​
 added

*   Approach 1. Add Census tract information to EHR data
“we currently don't have the governance to take approach 1”

*   Approach 2. Link health data to geocoded variables

   

RE: [gpc-informatics] #544: how to convert ACS raw variables to CAP variables (e.g. type of health insurance)?

[Dan Connolly]

The tract identifier identifies a geographic location with less than 20,000 
people in it, in most cases. That puts it on the PHI side of the "Safe Harbor" 
method, no?

Excerpt from "Guidance Regarding Methods for De-identification of Protected 
Health Information in Accordance with the Health Insurance Portability and 
Accountability Act (HIPAA) Privacy Rule"
https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html
 :

 the “Safe Harbor” method:
(2)(i) The following identifiers of the individual or of relatives, employers, 
or household members of the individual, are removed:
(B) All geographic subdivisions smaller than a state, including street address, 
city, county, precinct, ZIP code, and their equivalent geocodes, except for the 
initial three digits of the ZIP code if, according to the current publicly 
available data from the Bureau of the Census:
(1) The geographic unit formed by combining all ZIP codes with the same three 
initial digits contains more than 20,000 people; and
(2) The initial three digits of a ZIP code for all such geographic units 
containing 20,000 or fewer people is changed to 000

-- 
Dan


From: Bernard Black [bbl...@kellogg.northwestern.edu]
Sent: Monday, July 17, 2017 1:09 PM
To: gpc-dev@listserv.kumc.edu; Dan Connolly; Mei Liu; furmanc...@icnanotox.org; 
kosin...@mcw.edu
Cc: btay...@mcw.edu; vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook; Charon 
Gladfelter; Brennan Connolly; nicholas-c-sm...@uiowa.edu; 
phillip.ree...@utsouthwestern.edu; mo...@health.missouri.edu; 
danh...@regenstrief.org; Hillary Sandoval; George Kowalski
Subject: RE: [gpc-informatics] #544: how to convert ACS raw variables to CAP 
variables (e.g. type of health insurance)?

Census tract information *is* averaged, and is not PHI.
That is why Census is willing to release it.

Bernie
*
Bernard S. Black
bbl...@northwestern.edu
Nicholas D. Chabraja Professor, Northwestern University
 Pritzker School of Law
 Institute for Policy Research
 Kellogg School of Management, Finance Dep’t
Law School:  375 East Chicago Ave., Chicago IL 60611
Kellogg:  2211 Campus Drive, Evanston IL 60208
tel:  law:  312-503-2784; Kellogg:  847-491-5049; cell: 847-807-9599
papers on SSRN at:  http://ssrn.com/author=16042


-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Monday, July 17, 2017 12:11 PM
To: Dan Connelly <dconno...@kumc.edu>; mei...@kumc.edu; 
furmanc...@icnanotox.org; kosin...@mcw.edu
Cc: btay...@mcw.edu; Bernard Black <bbl...@kellogg.northwestern.edu>; 
vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook 
<lindsey.k...@northwestern.edu>; Charon Gladfelter 
<charon.gladfel...@northwestern.edu>; bconno...@kumc.edu; 
nicholas-c-sm...@uiowa.edu; phillip.ree...@utsouthwestern.edu; 
mo...@health.missouri.edu; danh...@regenstrief.org; hsando...@kumc.edu; George 
Kowalski <gkowal...@mcw.edu>
Subject: Re: [gpc-informatics] #544: how to convert ACS raw variables to CAP 
variables (e.g. type of health insurance)?

#544: how to convert ACS raw variables to CAP variables (e.g. type of health 
insurance)?
--+---
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  design-issue  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-stds |  Resolution:
 Keywords:|  Blocked By:
 Blocking:  598   |
--+---

Comment (by meiliu):

 Our most recent IRB protocol is in the attachment.
 - As noted in the protocol, "...variables such as income, educational  
attainment, likelihood of employment, poverty status, owner-occupied house  
value, and health insurance coverage derived from geocoded address data  will 
be used only as average values, not tied to any specific individual  but rather 
to study populations."
 - I did not find any language on sharing census tract information.
 I've discussed this with Tamara McMahon and agree that since census tract  may 
be PHI, we currently don't have the governance to take approach 1.

 Welcome any input from other sites.

--
Ticket URL: 
<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_trac_Project_ticket_544-23comment-3A15=DwICaQ=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE=wjt2QT-caC0BaQoqA-1jzlQgfOhmfVhDcHV0oV9o_sA=SiG0BJXb-ag0DCYa_svdEDeEWNVOJVkGOkV0JtvXSAY=
 > gpc-informatics 
<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_=DwICaQ=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE=wjt2QT-caC0BaQoqA-1jzlQgfOhmfVhDcHV0oV9o_sA=Mpnaed_RgiVlMRfvyIbhydJzr6UR3yEq9-l7Cbir8co=
 > Greater Plains N

gpc-dev 11 Jul agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 11 July shared 
notes
 - scribe: UTHSCSA




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW (regrets), MCRF, UMN, UNMC, UTHSCSA, 
UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UTHSCSA

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

*
 *   Next Meeting:  18 July. scribe?

*   Note LRU scribe schedule in 
#12

  2.  Milestone:cohort-char1
#570: 
collect expanded obesity cohort data 
comment:43:

 *   MCW ETA July 21

 *   UIOWA ETA? Census data news from 28 June meeting?

  3.  #596 targeted 
cancer therapy 
study due 18 July

 *   Re - in LOINC: Nick to consult with Dan about how to get REDCap to 
accept this.

 *   18 July deadline feeds participation / budget decisions

 *   Query 1: some records received from UIOWA, IU, KUMC, MCRF, MCW, MU, 
UNMC, UTSW

 *   Query 1: ETA from…

*   UMN

*   UTHSCSA

*   WISC

 *   Query 2: some records received from IU, MCRF, MU, UNMC, UIOWA

 *   Query 2: ETA from...

*   KUMC

*   MCW

*   UMN

*   UTHSCSA

*   UTSW

*   WISC

 *   Query 3: ETA?

  4.  
Milestone:cdm-cycle3

 *   #579 Data 
Characterization - Cycle 3 
Tracking

*   UNMC: “We had trouble running the SAS on our CDMV3.1 tables due to 
the fact that LAB_RESULT_CM increased to 192M records. Changing memory 
allocation in our SAS environment fixed that.”

*   PCORNET_TRIAL.PARTICIPANTID can be found on the CDM report in Mytrus

*   EDC report from UTSW received via sharing 
form

  5.  
Milestone:cdm-c2r2
 follow-up

 *   Please submit c2r2 EDC report to 
https://redcap.gpcnetwork.org/surveys/?s=9LT4KE8NFD
10 Received: MCRF, MCW, UNMC, KUMC, MU, IU, UMN, WISC, UTSW, CMH, UIOWA; 1 
pending:

*   UTHSCSA

 *   CMH - Dan to follow-up with technical contact at Cerner.
In progress

  6.  
Milestone:snow-shrine-2

 *   #604 Cert renewal: 
#605, 
#606, 
#607, 
#608, 
#609 KUMC, 
#610, 
#611, 
#612, 
#613 IU, 
#614, 
#615, 
#616

 *   #583: SNOW SCILHS Lab Metadata 
Expansion show and 
tell?

  7.  
milestone:grouse-resdac-2

 *   #595 
collect i2b2 datamarts for 
GROUSE: UTSW, MCRF

  8.  patient 
registries   
Tamara McMahon

 *   UNMC - McClay 12:57:29 
CDT

 *   Other sites...




--
Dan

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gpc-dev 27 June agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 27 June shared 
notes
 - scribe: MU




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: MU

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

*   #384 (ADAPTABLE teleconference records) 
closed

*   #541 (ADAPTABLE Enrollment Tracking - REDCap) 
closed

*   #574 (ADAPTABLE new computable phenotype total eligible) 
closed

 *   Next Meeting:  4 July? scribe?

*   Note LRU scribe schedule in 
#12

  2.  #570: collect expanded obesity cohort data 
comment:43:

 *   MCW ETA June 20th

 *   UIOWA ETA?

  3.  #596 targeted 
cancer therapy study - how to fulfill feasibility data 
request?

 *   Nick to work with Tamara to set up data access groups

*   Smith Fri Jun 23 
16:49

 *   Re - in LOINC: Nick to consult with Dan about how to get REDCap to 
accept this.

 *   Brad McDowell to check with Betsy whether early August is soon enough

*   “We would like the sites to proceed with Query 1 (which draws only 
from registry data to provide counts of tumors). At the last call, I was asked 
to provide a due date, and we hope to have the Query 1 results by Tuesday, June 
27. Please advise if this will be a problem.” -- Brad M. 16 Jun

 *   Each site gather constraints; be prepared to answer “when can you get 
this done?”

  4.  
Milestone:cdm-cycle3

 *   Question from George K. (MCW) about portion relating to Oracle 
interfacing with SAS.  Will follow up with email.

 *   Running the PCORNet EDC SAS on 
Linux   Michael 
Prittie

 *   #589 
principal diagnosis 10% threshold in PCORNet 
CDM

 *   #579 Data 
Characterization - Cycle 3 
Tracking

 *   Question about PRESCRIBING Table 
RX_QUANTITY_UNIT 
  Russ Waitman

 *   PCORnet CDRN's - We should 
talk!   
Verhagen, Laurel A

  5.  
Milestone:cdm-c2r2
 follow-up

 *   IU - Tony to share our i2p-transform changes.
#603 (Indiana - i2p Transform enhancements / 
replacement) 
created, closed fixed.

 *   Please submit c2r2 EDC report to 
https://redcap.gpcnetwork.org/surveys/?s=9LT4KE8NFD
10 Received: MCRF, MCW, UNMC, KUMC, MU, IU, UMN, WISC, UTSW, CMH; 2 pending:

*   IOWA working on this now (6 Jun)

*   UTHSCSA - by end of June

 *   CMH - Dan to follow-up with technical contact at Cerner.
In progress

  6.  
Milestone:snow-shrine-2

 *   SNOW SHRINE due 
date?   McClay, 
James C “We didn't budget for all this …”

*   JRC to suggest to McClay to talk with other PIs about SHRINE effort 
level in governing council (Dan to suggest likewise to RW)

 *   #604 Cert renewal: 
#605, 
#606, 
#607, 
#608, 

RE: CDM 3.1 beta (#578) [was: GPC-Dev meeting 6/20 - Canceled]

[Dan Connolly]

beta report? Is that different from the issue tracker Laurel referred us to in 
https://informatics.gpcnetwork.org/trac/Project/ticket/578#comment:11 ?

-- 
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Debbie Yoshihara 
[dlyos...@wisc.edu]
Sent: Tuesday, June 20, 2017 9:18 AM
To: Verhagen, Laurel A; gpc-dev@listserv.kumc.edu
Subject: Re: GPC-Dev meeting 6/20 - Canceled

Thanks Laurel!


Especially for the beta test CDM 3.1 Diagnostic Query.

Any chance we can get the beta report too ?


--- Debbie



From: Gpc-dev  on behalf of Verhagen, Laurel 
A 
Sent: Monday, June 19, 2017 5:18 PM
To: gpc-dev@listserv.kumc.edu
Subject: GPC-Dev meeting 6/20 - Canceled


Hi everyone,



Due to lack of email traffic in the past week, we will CANCEL the GPC-DEV 
meeting tomorrow (6/20) at 11:00.



Please use this extra time to get caught up on requests for your site, 
specifically the following:



· GROUSE - 
#595

· Ht/Wt data request - 
#570

· SHRINE Cert Renewal: 
#605, 
#606, 
#607, 
#608, 
#609, 
#610, 
#611, 
#612, 
#613, 
#614, 
#615, 
#616

· DCQ Cycle 3 - CDM v3.1 Diagnostic Query is available on 
iMeetCentral



Report progress via Trac as appropriate.



Thanks,

Laurel



Laurel Verhagen | Biomedical Informatics Research Center | Marshfield Clinic 
Research Institute | 715-221-6433 | 
verhagen.lau...@marshfieldresearch.org




The contents of this message may contain private, protected and/or privileged 
information. If you received this message in error, you should destroy the 
e-mail message and any attachments or copies, and you are prohibited from 
retaining, distributing, disclosing or using any information contained within. 
Please contact the sender and advise of the erroneous delivery by return e-mail 
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Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev

RE: Cancer CRG DROC Request presentation for GPC Dev call 06/13/2017

[Dan Connolly]

The assumptions slide is quite handy.

Regarding "That each site has the ability to run a query that joins both the 
CDM and i2b2" we can do that, but our CDM is de-identified, i.e. date-shifted 
by up to a year, so the years are going to be fuzzy. Is that good enough? Or 
are we going to need to un-shift the dates like we did for 
#448?

I only skimmed the remaining slides, but I didn't see anything about date 
(un-)shifting.

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Smith, Nicholas 
C [nicholas-c-sm...@uiowa.edu]
Sent: Monday, June 12, 2017 1:15 PM
To: gpc-dev@listserv.kumc.edu
Cc: Chrischilles, Elizabeth A
Subject: Cancer CRG DROC Request presentation for GPC Dev call 06/13/2017

Good afternoon, everyone:

For tomorrow’s dev call I have put together a presentation regarding ticket 
#596 (DROC Request from Cancer CRG: Preliminary feasibility query for study of 
use of targeted cancer therapy).

Here is the original DROC request, 
https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/596/DROC%20request%20-%20prelim%20feasibility%20targeted%20cancer%20tx-18MAY2017.docx

I have translated this DROC request into 3 separate queries that need to be run 
at each site.  The queries are contained within the presentation.  These 
queries evaluate both the CDM and i2b2.  I have written versions of the 3 
queries for MSSQL and Oracle although I was not able to test the Oracle queries 
since we are not an Oracle site.

Here is the presentation for tomorrow’s dev call, 
https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/596/DROC%20Breast%20Cancer%20Queries.pptx

Talk to you all tomorrow!


[cid:image002.jpg@01D2E37D.FF9D1EF0]

Nicholas C. Smith, MS
Senior Database Architect
Institute for Clinical & Translational Science 
(http://www.icts.uiowa.edu)
Email:  nicholas-c-sm...@uiowa.edu
Phone:  319-467-8173




Notice: This UI Health Care e-mail (including attachments) is covered by the 
Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only 
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gpc-dev 13 Jun agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 13 Jun shared 
notes<https://docs.google.com/document/d/1hrvKrMwdWm-i46I48a30jvGCqD5hvlzUjdyYBmgRMDs/edit>;
 scribe: IU




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

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

 *   roll: all 12 
DevTeams<https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams> 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: IU

*   regrets: CMH for 2 weeks

 *   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)

*   #602 (SNOW SHRINE authorization and governance) 
created<https://informatics.gpcnetwork.org/trac/Project/ticket/602>

 *   Next Meeting:  20 June? 27 June? scribe: MU? UTHSCSA?

*   Note LRU scribe schedule in 
#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:97>

*   i2b2 tranSMART Foundation 2017 
Symposium<http://transmartfoundation.org/the-i2b2-transmart-foundation-2017-symposium/>
 - DC, RW, MW to attend

  2.  Please complete ADAPTABLE tables by June 
14<http://listserv.kumc.edu/pipermail/gpc-dev/2017q2/004037.html>   Dan Connolly

  3.  #596<https://informatics.gpcnetwork.org/trac/Project/ticket/596> targeted 
cancer therapy study - how to fulfill feasibility data request?
<https://informatics.gpcnetwork.org/trac/Project/ticket/596>Nick Smith (and 
company?) to present

  4.  
Milestone:cdm-c2r2<https://informatics.gpcnetwork.org/trac/Project/milestone/cdm-c2r2>
 follow-up

 *   IU - Tony to share our i2p-transform changes.
#603 (Indiana - i2p Transform enhancements / 
replacement)<https://informatics.gpcnetwork.org/trac/Project/ticket/603> 
created, closed fixed.

 *   Please submit c2r2 EDC report to 
https://redcap.gpcnetwork.org/surveys/?s=9LT4KE8NFD
10 Received: MCRF, MCW, UNMC, KUMC, MU, IU, UMN, WISC, UTSW, CMH; 2 pending:

*   IOWA working on this now (6 Jun)

*   UTHSCSA - by end of June

 *   CMH - Dan to follow-up with technical contact at Cerner.
In progress

  5.  
Milestone:cdm-cycle3<https://informatics.gpcnetwork.org/trac/Project/milestone/cdm-cycle3>

 *   Question from George K. (MCW) about portion relating to Oracle 
interfacing with SAS.  Will follow up with email.

  6.  
Milestone:snow-shrine-2<https://informatics.gpcnetwork.org/trac/Project/milestone/snow-shrine-2>

 *   SNOW SHRINE due 
date?<http://listserv.kumc.edu/pipermail/gpc-dev/2017q2/004011.html>   McClay, 
James C “We didn't budget for all this …”

*   JRC to suggest to McClay to talk with other PIs about SHRINE effort 
level in governing council (Dan to suggest likewise to RW)

 *   #604 Cert renewal: 
#605<https://informatics.gpcnetwork.org/trac/Project/ticket/605>, 
#606<https://informatics.gpcnetwork.org/trac/Project/ticket/606>, 
#607<https://informatics.gpcnetwork.org/trac/Project/ticket/607>, 
#608<https://informatics.gpcnetwork.org/trac/Project/ticket/608>, 
#609<https://informatics.gpcnetwork.org/trac/Project/ticket/609>, 
#610<https://informatics.gpcnetwork.org/trac/Project/ticket/610>, 
#611<https://informatics.gpcnetwork.org/trac/Project/ticket/611>, 
#612<https://informatics.gpcnetwork.org/trac/Project/ticket/612>, 
#613<https://informatics.gpcnetwork.org/trac/Project/ticket/613>, 
#614<https://informatics.gpcnetwork.org/trac/Project/ticket/614>, 
#615<https://informatics.gpcnetwork.org/trac/Project/ticket/615>, 
#616<https://informatics.gpcnetwork.org/trac/Project/ticket/616>

  7.  
milestone:grouse-resdac-2<https://informatics.gpcnetwork.org/trac/Project/milestone/grouse-resdac-2>

 *   #618<https://informatics.gpcnetwork.org/trac/Project/ticket/618> 
collect WISC i2b2 repository copy for 
GROUSE<https://informatics.gpcnetwork.org/trac/Project/ticket/618>: “In an 
effort to share "minimum necessary" data, WISC plans to restrict their 
repository submission to the intersection of their population and the cohort 
from CMS. In order to supply the intersection, KUMC needs the crosswalk 
(#581<https://informatics.gpcnetwork.org/trac/Project/ticket/581>) derived from 
WISC's finder file 
(#562<https://informatics.gpcnetwork.org/trac/Project/ticket/562>).”

*   #581<https://informatics.gpcnetwork.org/trac/Project/ticket/581> 
“the request for the 2nd finder file 
(#581<https://informatics.gpcnetwork.org/trac/Proj

FW: GPC Dev Weely Teleconference

[Dan Connolly]

BEGIN:VCALENDAR
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ORGANIZER;CN=Dan Connolly;SENT-BY="MAILTO:mo...@health.missouri.edu":MAILTO:d
 conno...@kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN="Green, Ti
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 kumc.edu:MAILTO:hweed...@kumc.edu
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 w.edu:MAILTO:sup...@mcw.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=LHERBELIN
 @kumc.edu:MAILTO:lherbe...@kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=gpc-dev@l
 istserv.kumc.edu:MAILTO:gpc-dev@listserv.kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=JStatland
 @kumc.edu:MAILTO:jstatl...@kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=lfitzmaur
 i...@cmh.edu:MAILTO:lfitzmaur...@cmh.edu
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 u...@uiowa.edu:MAILTO:monika-ah...@uiowa.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=ellefson.
 j...@mcrf.mfldclin.edu:MAILTO:ellefson@mcrf.mfldclin.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=Cory.Gass
 n...@cerner.com:MAILTO:cory.gass...@cerner.com
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 @kumc.edu:MAILTO:vleona...@kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=rwaitman@
 kumc.edu:MAILTO:rwait...@kumc.edu
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 cw.edu:MAILTO:btay...@mcw.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=ngraham@k
 umc.edu:MAILTO:ngra...@kumc.edu
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 @kumc.edu:MAILTO:bzscho...@kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=Lindsay.C
 ow...@utsouthwestern.edu:MAILTO:lindsay.cow...@utsouthwestern.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=badagarla
 @kumc.edu:MAILTO:badaga...@kumc.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=Lori.Brow
 n...@cerner.com:MAILTO:lori.br...@cerner.com
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN="Popescu, 
 Mihail":MAILTO:popes...@health.missouri.edu
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=EMendonca
 @uwhealth.org:MAILTO:emendo...@uwhealth.org
ATTENDEE;ROLE=REQ-PARTICIPANT;PARTSTAT=NEEDS-ACTION;RSVP=FALSE;CN=meiliu@ku
 mc.edu:MAILTO:mei...@kumc.edu
ATTACH:CID:238835680EA5F649B6BFF543382F5349@kumc.edu
DESCRIPTION;LANGUAGE=en-US:\n\n\n\n____
 \nFrom: Dan Connolly\nSent: Tuesday\, October 6\, 2015 7:27:51 PM UTC\nTo:
  Dan Connolly\; gpc-dev@listserv.kumc.edu\nCc: Gassner\,Cory\; Hillary Wee
 dman\; Kieran Pemberton\; Ahuja\, Monika\; Taylor\, Bradley\; Ellefson\, J
 oseph\; Nathan Graham\; Russ Waitman\; Brittany Zschoche\; Mei Liu\; Vince
 nt Leonardo\; Lindsay Cowell\; Mosa\, Abu S.\; Popescu\, Mihail\; Laura He
 rbelin\; Jeffrey Statland\; Green\, Timothy A.\; Bhargav Adagarla\; Fitzma
 urice\, Laura (MD)\; Uppal\, Sabrina\; Brown\,Lori\; Mendonca Eneida\nSubj
 ect: GPC Dev Weely Teleconference\nWhen: Tuesday\, June 6\, 2017 4:00 PM-5
 :00 PM.\nWhere: https://global.gotomeeting.com/meeting/join/817393381\n\nW
 hen: Occurs every Tuesday from 11:00 AM to 12:00 PM effective 1/6/2015 unt
 il 9/24/2018. (UTC-06:00) Central Time (US & Canada)\nWhere: https://globa
 l.gotomeeting.com/meeting/join/817393381\n\n*~*~*~*~*~*~*~*~*~*\n\nExtendi
 ng the series for the duration of phase 2...\n\n1. Please join my meeting.
 \nhttps://global.gotomeeting.com/meeting/join/817393381\n\n2. Use your mic
 rophone and speakers (VoIP) - a headset is recommended. Or\, call in using
  your telephone.\nUnited States (Toll-free): +1 (571) 317-3131\n\nAccess C
 ode: 817-393-381\nAudio PIN: Shown after joining the meeting\n\nMeeting ID
 :817-393-381\n\nAn agenda is due to the gpc-dev mailing list a day in adva
 nce\n  http://listserv.kumc.edu/pipermail/gpc-dev/\n\nFor more information
 \, see:\nhttps://informatics.gpcnetwork.org/trac/Project/wiki/SoftwareDev#
 next-agenda\n
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RECURRENCE-ID;TZID=Customized Time Zone:20170606T11
SUMMARY;LANGUAGE=en-US:FW: GPC Dev Weely Teleconference
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DTEND;TZID=Customized Time

gpc-dev 6 Jun agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   ​gpc-dev 6 Jun meeting shared 
notes<https://docs.google.com/document/d/1XVZ73Zt3iRgvQla7BX-rBSnojJJARnIe068cbidrUdY/edit>;
 scribe: UNMC




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

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

 *   roll: all 12 
DevTeams<https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams> 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UNMC

 *   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)

*   #602 (SNOW SHRINE authorization and governance) 
created<https://informatics.gpcnetwork.org/trac/Project/ticket/602>

 *   Next Meeting:  13 June? scribe: CMH? IU?

*   Note LRU scribe schedule in 
#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:92>

  2.  
Milestone:cdm-c2r2<https://informatics.gpcnetwork.org/trac/Project/milestone/cdm-c2r2>
 Experience reports

 *   Please submit c2r2 EDC report to 
https://redcap.gpcnetwork.org/surveys/?s=9LT4KE8NFD
9 Received: MCRF, MCW, UNMC, KUMC, MU, IU, UMN, WISC, UTSW
3 pending: CMH, IOWA, UTHSCSA

 *   CMH - Dan to follow-up with technical contact at Cerner.

 *   IU - Tony to share our i2p-transform changes.

  3.  
Milestone:cdm-cycle3<https://informatics.gpcnetwork.org/trac/Project/milestone/cdm-cycle3>

 *   #578<https://informatics.gpcnetwork.org/trac/Project/ticket/578> DC 
Cycle 3 - Beta 
Testing<https://informatics.gpcnetwork.org/trac/Project/ticket/578> closed fixed
Query package v3.1 Issue 
tracker<https://pcornet.imeetcentral.com/drnoc-workgroups/folder/WzIwLDg5ODQzOThd/WzIsNTIzMTEwNDRd/>
 link provided

 *   #280<https://informatics.gpcnetwork.org/trac/Project/ticket/280> 
Medication ontology orgainzed by 
ingredient<https://informatics.gpcnetwork.org/trac/Project/ticket/280> - JRC 
provided positive experience getting NCD code from administrations in comment:27

 *   help moving CDM SAS to 
linux<http://listserv.kumc.edu/pipermail/gpc-dev/2017q2/004009.html>   Dan 
Connolly

  4.  
Milestone:cohort-char1<https://informatics.gpcnetwork.org/trac/Project/milestone/cohort-char1>
 (obesity cohort) due 12 Jun

 *   For #570<https://informatics.gpcnetwork.org/trac/Project/ticket/570> 
collect expanded obesity cohort data: demographics, income, insurance / 
financial class<https://informatics.gpcnetwork.org/trac/Project/ticket/570> - 
UNMC submitted 3 Jun; joins CMH, UMN, UTHSCSA (old?)

*   UIOWA - no one is in the Data Access Group

  5.  
Milestone:snow-shrine-2<https://informatics.gpcnetwork.org/trac/Project/milestone/snow-shrine-2>
 due 30 Jun

 *   SNOW SHRINE due 
date?<http://listserv.kumc.edu/pipermail/gpc-dev/2017q2/004007.html>   Gryzlak, 
Brian M

 *   SNOW SHRINE due 
date?<http://listserv.kumc.edu/pipermail/gpc-dev/2017q2/004011.html>   McClay, 
James C “We didn't budget for all this …”

  6.  
Milestone:next-d<https://informatics.gpcnetwork.org/trac/Project/milestone/next-d>
 next checkpoint: 12 Jun

 *   #546<https://informatics.gpcnetwork.org/trac/Project/ticket/546> 
Oracle port of 
NextDextractionCode_12.1.16.sql<https://informatics.gpcnetwork.org/trac/Project/ticket/546>
 GK making progress: 31 May 
7088f41<https://github.com/gkowalski/nextd-study-support/commit/7088f41d116bad56212d2472f0a8147a8a111e73>

 *   #544<https://informatics.gpcnetwork.org/trac/Project/ticket/544> how 
to convert ACS raw variables to CAP variables (e.g. type of health 
insurance)?<https://informatics.gpcnetwork.org/trac/Project/ticket/544> 
Unpacking STATA files from MPC in progress.

  7.  
Milestone:gpc-phase2-h5<https://informatics.gpcnetwork.org/trac/Project/milestone/gpc-phase2-h5>
 text notes

 *   #431<https://informatics.gpcnetwork.org/trac/Project/ticket/431> 
Deploy free text notes and de-identification at majority of GPC sites 
(milestone 2.12.1)<https://informatics.gpcnetwork.org/trac/Project/ticket/431> 
- “RW has secured an extension for milestone 2.12.1. The new due date is TBD”

 *   #573<https://informatics.gpcnetwork.org/trac/Project/ticket/573> 
de-identified text notes for on a cohort-by-cohort 
basis<https://informatics.gpcnetwork.org/trac/Project/ticket/573>

*   Brad to run mastectomy / operative notes sketch by GPC breast 
cancer researchers and refine / revise to get hypothesis etc.

*  

RE: SNOW SHRINE due date?

[Dan Connolly]

How much sites should expect to budget for SHINE is a very good question; in 
retrospect, perhaps I should have made it explicit long ago.

I expected it to be onerous based on a sort of "SHRINE war stories" panel I saw 
years ago at an i2b2 meeting.

Looking over how much time we've spent, I find a couple main internal tickets:

  *   #4544: 31 comments from Feb 20 to May 10 (fixed)
  *   #4291: 42 comments from Sep 21 to May 10 (ongoing)

Time corresponding to a comment ranges from a few minutes in a meeting to an 
hour to half a day. Work started in earnest after HackathonFour in January. So 
a ballpark figure is 4 person-weeks. And we're not done.

I have a vague memory that UTHSCSA estimated that getting SHRINE going didn't 
take much time. Perhaps their internal network security discussions were less 
involved? Is UTHSCSA on the SNOW SHRINE network yet?

Any other site that cares to give a ballpark time cost figure is more than 
welcome.

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of McClay, James C 
[jmcc...@unmc.edu]
Sent: Friday, June 02, 2017 11:41 AM
To: gpc-dev@listserv.kumc.edu
Subject: RE: SNOW SHRINE due date?

Is it just Nebraska or is the setup and configuration of the SHRINE node really 
onerous? Our sysadmin has put in HOURS and isn’t finished yet. We didn’t budget 
for all this trouble.

Anyone found an easy configuration process?
jm

From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan 
Connolly
Sent: Thursday, June 1, 2017 4:17 PM
To: Gryzlak, Brian M <brian-gryz...@uiowa.edu>; gpc-dev@listserv.kumc.edu
Subject: RE: SNOW SHRINE due date?

The due date for 
milestone:snow-shrine-2<https://informatics.gpcnetwork.org/trac/Project/milestone/snow-shrine-2>
 was April... it's now... um... May 29. You got your time machine installed and 
running, right?

I suppose June 30 should work. I tend to keep due dates on Mondays, in time for 
agenda prep for Tuesday calls, so I put June 26 in trac. That is: if you don't 
expect to make it by June 30, please let us know by June 26.

Juggling due dates SHRINE, CDM 3.1, and free text notes de-identification is 
tricky, so I expect to talk with Russ about the 
roadmap<https://informatics.gpcnetwork.org/trac/Project/roadmap> of milestones 
soon.

--
Dan

From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Gryzlak, Brian M 
[brian-gryz...@uiowa.edu]
Sent: Thursday, June 01, 2017 4:01 PM
To: gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>
Subject: SNOW SHRINE due date?
Can someone (Dan, Russ?) please weigh in on when it is expected that individual 
GPC sites should have their SNOW SHRINE nodes up?  Is June 30 a realistic and 
acceptable due date?

Thanks,
Brian

The information in this e-mail may be privileged and confidential, intended 
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help moving CDM SAS to linux

[Dan Connolly]

We're hitting these errors only on linux; anybody seen them?


1965: ERROR: Variable _FREQ_ is not on file WORK.STATS.
1966: ERROR: Invalid DROP, KEEP, or RENAME option on file WORK.STATS.
1967: ERROR: Variable _type_ is not on file WORK.STATS.
...


--
Dan

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RE: SNOW SHRINE due date?

[Dan Connolly]

The due date for 
milestone:snow-shrine-2
 was April... it's now... um... May 29. You got your time machine installed and 
running, right?

I suppose June 30 should work. I tend to keep due dates on Mondays, in time for 
agenda prep for Tuesday calls, so I put June 26 in trac. That is: if you don't 
expect to make it by June 30, please let us know by June 26.

Juggling due dates SHRINE, CDM 3.1, and free text notes de-identification is 
tricky, so I expect to talk with Russ about the 
roadmap of milestones 
soon.

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Gryzlak, Brian M 
[brian-gryz...@uiowa.edu]
Sent: Thursday, June 01, 2017 4:01 PM
To: gpc-dev@listserv.kumc.edu
Subject: SNOW SHRINE due date?

Can someone (Dan, Russ?) please weigh in on when it is expected that individual 
GPC sites should have their SNOW SHRINE nodes up?  Is June 30 a realistic and 
acceptable due date?

Thanks,
Brian
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FW: [gpc-informatics] #601: Advice on Oracle/SQL Server maintenance protocols

[Dan Connolly]

Good question, Jim. I don't know if I have much to offer by way of advice; I 
also feel like there's got to be a better way to get early notice of Oracle 
issues.

We have explored or are exploring several different approaches: (a) hire a DBA 
(b) hire a a consultant (c) use other Oracle expertise at KUMC (d) run away! 
and try postgres.

Hiring worked ok for a while, but attrition is a natural thing and finding a 
good fit is a challenge. We hired Burleson and had them do an Oracle health 
check http://www.dba-oracle.com/oracle_health_check.htm . We haven't found time 
to implement all of their recommendations. :-/ And we haven't managed to grant 
them access to do it for us. :-/

A big reason we use Oracle is that KUMC has an enterprise license. We made an 
arrangement with another IT group at KUMC to get some time from their DBAs. 
That's going pretty well recently.

Meanwhile, we're keeping an eye on postgres and trying not to invest in Oracle 
techniques that don't port readily to postgres.

-- 
Dan


From: GPC Informatics [d...@madmode.com]
Sent: Tuesday, May 30, 2017 3:36 PM
To: campb...@unmc.edu; Dan Connolly
Subject: [gpc-informatics] #601: Advice on Oracle/SQL Server maintenance 
protocols

#601: Advice on Oracle/SQL Server maintenance protocols
---+---
  Reporter:  campbell  |  Owner:  dconnolly
  Type:  design-issue  | Status:  new
  Priority:  minor |  Milestone:
 Component:  dev-tools |   Keywords:
Blocked By:|   Blocking:
---+---
 We have our i2b2 platforms on Oracle.  Our support shop has little
 experience with maintaining production environments  for the identified
 and deidentified platforms.  Last week we experienced prolonged downtime
 due to file count overruns in Oracle that could have been prevented had we
 monitoring and management routines in place.  Can any of our colleagues
 across GPC give us advice on Oracle maintenance procedures we should be
 establishing as part of our operating procedures?
 Jim

--
Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/601>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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FW: GPC Dev Weely Teleconference

[Dan Connolly]

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 dman\; Kieran Pemberton\; Ahuja\, Monika\; Taylor\, Bradley\; Ellefson\, J
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 urice\, Laura (MD)\; Uppal\, Sabrina\; Brown\,Lori\; Mendonca Eneida\nSubj
 ect: GPC Dev Weely Teleconference\nWhen: Tuesday\, May 30\, 2017 4:00 PM-5
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DESCRIPT

gpc-dev 30 May agenda and meeting notes

[Dan Connolly]

I only know this much of the agenda; suggestions are welcome:

  *   gpc-dev 30 May shared meeting 
notes;
 scribe: UIOWA




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UIOWA

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

*   ...

 *   Next Meeting:  6 June; scribe???

*   Note LRU scribe schedule in 
#12

  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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RE: combining notes

[Dan Connolly]

Do you use SQL to do the iterating and concatenating? Or something else like 
python or Java?

That is: can this query be used as the input query to the deid software? Or is 
there a separate prep step to put the concatenation results back in the DB?

-- 
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Kowalski, George 
[gkowal...@mcw.edu]
Sent: Wednesday, May 24, 2017 5:00 PM
To: gpc-dev@listserv.kumc.edu
Subject: combining notes

All ,

Per yesterday’s call:  Not much to the code to combine text notes . Our main 
query is :

SELECT
pm.date_off,
hnt.*
FROM
hno_note_text hnt
LEFT OUTER JOIN
patient_mapping pm
ON
hnt.pat_id = pm.pat_id
WHERE
hnt.note_id IS NOT NULL
AND hnt.pat_id IS NOT NULL
ORDER BY
hnt.note_id,
hnt.note_csn_id,
hnt.line

we join to patient_mapping as that contains the date offset we store per user 
for shifting dates.

With this result set we iterate over the results and concatenate that rows text 
if the CSN ID of that row matches the last row. Then write it to a matching 
table (except it has an extra column for the date_offset and an empty column 
for de-identified notes that we generate later )  The only trick we found is 
that when combining rows of text , we had to place a space between each row or 
we generated  concatenated words.

G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu
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RE: Linking Geocoding data with i2b2

[Dan Connolly]

At KUMC, reproducing MU's work on i2b2 integration remains largely on our TODO 
list.

But as for tips for working with the data, we've done enough to be able to do 
ad-hoc queries such as "count HERON patients by income group":

select 'Over' || to_char(hi.dollar_group, '$999,999') income_group, sex_cd, 
count(patient_num)
from nightherondata.patient_dimension pat
join household_income hi on substr(zip_cd, 1, 5) = hi.zcta5
group by sex_cd, hi.dollar_group
having count(patient_num) > 100
order by dollar_group, sex_cd
;

... where household_income is a cache of some of the census data:

create materialized view household_income as
select zcta5, UHD001 dollars
 , case
   when UHD001 < 35000 then 0
   when UHD001 < 42000 then 35000
   when UHD001 < 52000 then 42000
   when UHD001 < 59000 then 52000
   when UHD001 < 74000 then 59000
   else 74000
   end dollar_group
from acs_zcta_2
;


For tables such as acs_zcta_2, we're currently using external access tables; 
i.e. selecting from the Oracle tables reads directly from the .gz files. This 
is slow, but caches such as household_income work fine.

I shared the table definitions in
https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/509/geo_acs_tables.sql

They're generated using...
https://github.com/dckc/i2b2-geo/blob/master/census_schema_gen.py

The median income query above just uses zip code; to zero in to census block 
resolution, we'd need to join patient address to the table of geocoded 
addresses.

For the table of geocoded addresses, what I did amounts to the same thing 
George did; perhaps a bit over-engineered.

I wrote this script:
https://github.com/dckc/i2b2-geo/blob/master/geo_addr_stage.py 4f537fc on Jan 4

and ran it in a jenkins job; the log shows:

python geo_addr_stage.py MPC_ACCOUNT geocoded_kumc
14:33:26 INFO: Counting records in geocoded_kumc.txt from geocoded_kumc.zip
14:33:32 INFO: loading 1237329 records into table geocoded_kumc of DB 
MPC_ACCOUNT...
14:33:32 INFO: creating table geocoded_kumc with 32 columns
14:33:33 INFO: inserting 1 records into geocoded_kumc...
14:33:33 INFO: 1 of 1237329 records (0.8%)
...
14:36:03 INFO: inserting 7327 records into geocoded_kumc...
14:36:03 INFO: 1237327 of 1237329 records (100.0%)
Finished: SUCCESS


--- 
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Kowalski, George 
[gkowal...@mcw.edu]
Sent: Wednesday, May 24, 2017 1:24 PM
To: Phillip Reeder
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: Linking Geocoding data with i2b2

Phil,

I just created the table  in oracle  , shooting from the hip :

CREATE TABLE
MCW_GEOCODING
(
OID INTEGER,
JOIN_COUNT INTEGER,
TARGET_FID INTEGER,
LOC_NAME VARCHAR2(200),
STATUS VARCHAR2(200),
SCORE INTEGER,
MATCH_TYPE VARCHAR2(200),
X FLOAT(126),
Y FLOAT(126),
...
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getting gpc-dev work done (vs. asking for agenda items)

[Dan Connolly]

Periodic public service announcement, prompted by several recent messages 
putting me in the critical path unnecessarily...

The sources for gpc-dev weekly agenda 
items
 are:

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

If you find yourself writing to me with a subject like "Item for today's call," 
please move the fact that you'd like to discuss it on the call to a p.s. in 
your message and put the substance of what you want to discuss in the subject 
and body and send it to all concerned (e.g. via gpc-dev@listserv.kumc.edu).

Or, as I put it back in my March 2016 
message:
it's best to start the discussion in substance in email, leaving aside the 
question of whether we'll talk about it on a phone call. If, when you see the 
agenda come out, you don't see your item on it and you're not satisfied with 
the email discussion, you can always ask for it to be added.
--
Dan

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RE: Next-D labs

[Dan Connolly]

The bulk of KUMC's glucose data (100K+ patients) seems to be mapped to 2340-8. 
You're sure you want to exclude it?

The only intersection between the remaining codes and what's used at KUMC is 
2339-0 (6K patients).

--
Dan


From: Kho, Abel [abel@nm.org]
Sent: Monday, May 22, 2017 1:10 PM
To: Dan Connolly; Campbell, James R; Al'ona Furmanchuk
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: Next-D labs


Yes except the two glucose by test strip (below) should be removed.  Jim, I 
noticed this after our conversation but to be consistent with removing glucose 
by finger stick, I removed these.


Random Glucose2341-6Glucose [Mass/Volume] in blood by test strip method
Random glucose2340-8Glucose [Mass/Volume] in blood by automated test 
strip



From: Dan Connolly <dconno...@kumc.edu>
Sent: Monday, May 22, 2017 12:46 PM
To: Campbell, James R; Kho, Abel; Al'ona Furmanchuk
Cc: gpc-dev@listserv.kumc.edu
Subject: RE: Next-D labs

Ah... somehow I had miss this, Jim. Yes, the 2nd worksheet is the sort of thing 
I can use.

Dr. Kho, does this include the merging you were talking about?

http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20170510/055fa3e4/attachment-0001.xlsx

--
Dan


From: Campbell, James R [campb...@unmc.edu]
Sent: Wednesday, May 10, 2017 9:42 AM
To: Dan Connolly
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: Next-D labs


Use the second worksheet in the enclosed Excel Dan


From: Dan Connolly <dconno...@kumc.edu>
Sent: Wednesday, May 10, 2017 9:17:44 AM
To: Kho, Abel; Campbell, James R; Black, Bernard (NU); Cook, Lindsey (NU)
Cc: gpc-dev@listserv.kumc.edu
Subject: RE: Next-D labs

This is great to have, but as tried to say in the NEXT-D - 4/6/17 GPC-CAP 
Bi-Weekly Meeting, we need something we can save as CSV and load into a 
database. I'm not sure what happens to strikethru formatting when this is saved 
to CSV; separate columns with yes/no or 1/0 would be more straightforward. I 
suppose I could have been more clear; the notes only say "New format will 
specify explicitly type (random/fasting) of glucose measurement as well as 
yes/no decision on keeping lab on the list ".

If one of you finds a moment to add such columns, that would be great; 
otherwise, clearly there are many of us that can make such a tweak. Alona? Mei? 
George? Maybe I'll find the time...

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Kho, Abel 
[abel@nm.org]
Sent: Wednesday, May 10, 2017 8:56 AM
To: Campbell, James R; Black, Bernard (NU); Cook, Lindsey (NU)
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: Next-D labs


Jim,

Likewise and thanks for your insight.  I agree with your annotated version (I 
did the same after our discussion and fortunately they match 1:1).

Too bad about next week and we'll send out a draft agenda to you later today.  
We may have to update by f/u email with the call in number though as it gets 
closer to the date.

Thanks,

Abel



From: Campbell, James R <campb...@unmc.edu>
Sent: Wednesday, May 10, 2017 8:48 AM
To: Kho, Abel; Black, Bernard (NU); Cook, Lindsey (NU)
Cc: gpc-dev@listserv.kumc.edu
Subject: Next-D labs

Abel
It was a pleasure talking with you this morning.  I enclose a spreadsheet 
summarizing what I think was our discussion on blood sugars and appropriate 
codes for Next-D.  Please correct any misconceptions I might have included.

I checked my schedule and I have teaching responsibilities next Tuesday.  I 
would be happy to participate as much as possible by telecom if you think I 
might be helpful.  Can you forward a detailed agenda for Tuesday so that I 
might plan my time?
Jim

The information in this e-mail may be privileged and confidential, intended 
only for the use of the addressee(s) above. Any unauthorized use or disclosure 
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please delete it and immediately contact the sender.

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RE: Next-D labs

[Dan Connolly]

Ah... somehow I had miss this, Jim. Yes, the 2nd worksheet is the sort of thing 
I can use.

Dr. Kho, does this include the merging you were talking about?

http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20170510/055fa3e4/attachment-0001.xlsx

--
Dan


From: Campbell, James R [campb...@unmc.edu]
Sent: Wednesday, May 10, 2017 9:42 AM
To: Dan Connolly
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: Next-D labs


Use the second worksheet in the enclosed Excel Dan


From: Dan Connolly <dconno...@kumc.edu>
Sent: Wednesday, May 10, 2017 9:17:44 AM
To: Kho, Abel; Campbell, James R; Black, Bernard (NU); Cook, Lindsey (NU)
Cc: gpc-dev@listserv.kumc.edu
Subject: RE: Next-D labs

This is great to have, but as tried to say in the NEXT-D - 4/6/17 GPC-CAP 
Bi-Weekly Meeting, we need something we can save as CSV and load into a 
database. I'm not sure what happens to strikethru formatting when this is saved 
to CSV; separate columns with yes/no or 1/0 would be more straightforward. I 
suppose I could have been more clear; the notes only say "New format will 
specify explicitly type (random/fasting) of glucose measurement as well as 
yes/no decision on keeping lab on the list ".

If one of you finds a moment to add such columns, that would be great; 
otherwise, clearly there are many of us that can make such a tweak. Alona? Mei? 
George? Maybe I'll find the time...

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Kho, Abel 
[abel@nm.org]
Sent: Wednesday, May 10, 2017 8:56 AM
To: Campbell, James R; Black, Bernard (NU); Cook, Lindsey (NU)
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: Next-D labs


Jim,

Likewise and thanks for your insight.  I agree with your annotated version (I 
did the same after our discussion and fortunately they match 1:1).

Too bad about next week and we'll send out a draft agenda to you later today.  
We may have to update by f/u email with the call in number though as it gets 
closer to the date.

Thanks,

Abel



From: Campbell, James R <campb...@unmc.edu>
Sent: Wednesday, May 10, 2017 8:48 AM
To: Kho, Abel; Black, Bernard (NU); Cook, Lindsey (NU)
Cc: gpc-dev@listserv.kumc.edu
Subject: Next-D labs

Abel
It was a pleasure talking with you this morning.  I enclose a spreadsheet 
summarizing what I think was our discussion on blood sugars and appropriate 
codes for Next-D.  Please correct any misconceptions I might have included.

I checked my schedule and I have teaching responsibilities next Tuesday.  I 
would be happy to participate as much as possible by telecom if you think I 
might be helpful.  Can you forward a detailed agenda for Tuesday so that I 
might plan my time?
Jim

The information in this e-mail may be privileged and confidential, intended 
only for the use of the addressee(s) above. Any unauthorized use or disclosure 
of this information is prohibited. If you have received this e-mail by mistake, 
please delete it and immediately contact the sender.

This message and any included attachments are intended only for the addressee. 
The information contained in this message is confidential and may constitute 
proprietary or non-public information under international, federal, or state 
laws. Unauthorized forwarding, printing, copying, distribution, or use of such 
information is strictly prohibited and may be unlawful. If you are not the 
addressee, please promptly delete this message and notify the sender of the 
delivery error by e-mail.

The information in this e-mail may be privileged and confidential, intended 
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RE: [gpc-informatics] #444: Pregnancy Status for NEXT-D

[Dan Connolly]

I suppose this question is to Jennifer Cai at UTSW; she doesn't seem to be 
copied. Mei, would you please add her to this thread?

Or perhaps you can answer, Phillip?

--
Dan


From: Al'ona Furmanchuk [furmanc...@icnanotox.org]
Sent: Thursday, May 18, 2017 11:30 AM
To: <gpc-dev@listserv.kumc.edu>
Cc: Nathan Graham; Laurel Verhagen; Dan Connolly; Sravani Chandaka; McNeeley, 
Todd Alexander; Mei Liu; Campbell, James R; Satyender Goel; Bernard Black; 
Charon Gladfelter
Subject: Re: [gpc-informatics] #444: Pregnancy Status for NEXT-D

Did I get it right that you guys have EPISODE table in your system that keeping 
track of different  conditions including pregnancy (SUM_BLK_TYPE_ID = 2).
The data into this table is collected as result of processing notes and other 
text type records. You do not use CPT, ICD and other codes in your algorithm 
defining pregnancy episodes. Right?

Do you upload this information to CONDITION table in your PCORNET CDM? If yes, 
we could add extra line to the code to pick this information when checking for 
pregnancy exclusion condition.

On Thu, May 18, 2017 at 11:14 AM, GPC Informatics 
<d...@madmode.com<mailto:d...@madmode.com>> wrote:
#444: Pregnancy Status for NEXT-D
--+---
 Reporter:  afurmanchuck  |   Owner:  afurmanchuck
 Type:  design-issue  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-stds |  Resolution:
 Keywords:|  Blocked By:
 Blocking:  546   |
--+---

Comment (by meiliu):

 Following is UTSW's approach to retrieve pregnancy data provided by
 Jennifer Cai on 5/18:
 

 Following are two tables to retrieve pregnancy data:

 EPISODE
 EPISODE_LINK

 Here is one script we used to retrieve the data

SELECT P.*, PAT_LINK_ID, EDD_INITIAL_DT, OB_WRK_EDD_DT,
 L.PAT_ENC_CSN_ID, E.COMMENTS,E.STICKY_NOTE_TEXT,E.PROVIDERS_COMMENT
FROM EPISODE E LEFT JOIN EPISODE_LINK  L ON L.EPISODE_ID = E.EPISODE_ID
 AND L.LINE = 1
  , LAUREN_SINGER_PAT_LIST P   -- this is our local temporary patient
 cohort table
  WHERE E.STATUS_C = 1
   AND P.PAT_ID = E.PAT_LINK_ID
   AND E.SUM_BLK_TYPE_ID = 2
   AND ((OB_WRK_EDD_DT > SYSDATE OR OB_WRK_EDD_DT IS NULL) AND (
 EDD_INITIAL_DT > SYSDATE OR EDD_INITIAL_DT IS NULL))
 --  order by concept_id

 --Note: Based on the data in table EPISODE where status = 1 (active) and
 SUM_BLK_TYPE_ID = 2 (pregnancy) and EDD > sysdate

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/444#comment:19>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics



--
Al’ona Furmanchuk, Ph.D.
Research Associate

Center for Health Information Partnerships,
Northwestern University, Feinberg School of Medicine
633 N. Saint Clair Street, 20th floor,
Chicago, IL 60611
Web: http://furmanchuk.com/
E-mail: alona.furmanc...@northwestern.edu<mailto:furmanc...@icnanotox.org>
Phone: 312-503-34281
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RE: gpc-dev 16 May agenda and meeting notes

[Dan Connolly]

I'm still not organized, but whatever happens, here's where to meet and where 
to take notes:

  *   gpc-dev 16 May shared 
notes<https://docs.google.com/document/d/1-Z_RySZ5_Xi78USq2m9ekLIHnFEl5uP3Ac6VVPtayEU/edit>;
 scribe: WISC
  *   11:00am Central Time.
​Meeting ID and access code: 
817-393-381<https://global.gotomeeting.com/meeting/join/817393381>; call +1 
(571) 317-3131

________
From: Dan Connolly
Sent: Monday, May 15, 2017 3:52 PM
To: gpc-dev@listserv.kumc.edu
Subject: gpc-dev 16 May agenda and meeting notes

I'm way behind on putting an agenda together.

Please plan to meet, though. Same bat-time, same bat-channel.

--
Dan

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gpc-dev 16 May agenda and meeting notes

[Dan Connolly]

I'm way behind on putting an agenda together.

Please plan to meet, though. Same bat-time, same bat-channel.

--
Dan

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RE: Geo Coding

[Dan Connolly]

I should perhaps invest in better documentation in this area...

#140 is sort of a "solve all problems related to geocoding" ticket... the 
finite task of distributing the address->block mappings was separated out as 
#350<https://informatics.gpcnetwork.org/trac/Project/ticket/350>.

Data was sent out soon after Oct 2, 2015 (comment:6), and by Oct 13 
(comment:10<https://informatics.gpcnetwork.org/trac/Project/ticket/350#comment:10>)
 someone from UNMC had confirmed receipt. The ticket doesn't say exactly who; 
let's check meeting records... "JRC: UNMC got it" says the notes from 13 
Oct<http://listserv.kumc.edu/pipermail/gpc-dev/2015q4/002130.html>.

In comment:16, I see I made note of a filename; ours was geocoded_kumc.zip 
95.95 MB, which strongly suggests yours was geocoded_unmc.zip perhaps rougly 
the same size.

--
Dan


From: Gardner, Bret J [bret.gard...@unmc.edu]
Sent: Thursday, May 11, 2017 12:22 PM
To: gpc-dev@listserv.kumc.edu
Cc: Dan Connolly
Subject: Geo Coding

 UNMC is working through geo-coding and linking to socioeconomic status.  
We have obtained necessary median income information on a per census block 
basis, however, we do not have patient addresses mapped to census blocks.  
Reviewing Ticket #140, comment 43, we are wondering how to access the geo-coded 
patient address information.  The comment indicates KUMC has a file with this 
information.
 Please point us to this file.
Thank you,

Bret J. Gardner
Graduate Student
University of Nebraska Medical Center
MD/PhD Scholars Program
bret.gard...@unmc.edu<mailto:bret.gard...@unmc.edu>
801-455-5168 (cell)


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RE: question on GROUSE Extract

[Dan Connolly]

Good question, George.

Russ?

-- 
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Kowalski, George 
[gkowal...@mcw.edu]
Sent: Tuesday, May 09, 2017 7:34 PM
To: gpc-dev@listserv.kumc.edu
Subject: question on GROUSE Extract

All,

Per todays call referencing ticket 
(https://informatics.gpcnetwork.org/trac/Project/ticket/595 ), we've had 
further discussion here at MCW and have a question.

Is this extract only for Grouse at this time or is this going to be also be 
used for the "Cancer CRG" with this initial pull?

We have had previous communications with Betsy,  and conveyed to her that our 
data is currently missing the Meds Admin data required for chemo dosing . 
Getting this data into our I2B2 instance is 2 months out. If this is not a 
requirement now, we can dump the requested files and upload them to KU. But if 
the expectation is that this data will be usable now for the Cancer CRG, we 
suggest that we hold off until we get that data loaded.?

George

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RE: Next-D labs

[Dan Connolly]

This is great to have, but as tried to say in the NEXT-D - 4/6/17 GPC-CAP 
Bi-Weekly Meeting, we need something we can save as CSV and load into a 
database. I'm not sure what happens to strikethru formatting when this is saved 
to CSV; separate columns with yes/no or 1/0 would be more straightforward. I 
suppose I could have been more clear; the notes only say "New format will 
specify explicitly type (random/fasting) of glucose measurement as well as 
yes/no decision on keeping lab on the list ".

If one of you finds a moment to add such columns, that would be great; 
otherwise, clearly there are many of us that can make such a tweak. Alona? Mei? 
George? Maybe I'll find the time...

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Kho, Abel 
[abel@nm.org]
Sent: Wednesday, May 10, 2017 8:56 AM
To: Campbell, James R; Black, Bernard (NU); Cook, Lindsey (NU)
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: Next-D labs


Jim,

Likewise and thanks for your insight.  I agree with your annotated version (I 
did the same after our discussion and fortunately they match 1:1).

Too bad about next week and we'll send out a draft agenda to you later today.  
We may have to update by f/u email with the call in number though as it gets 
closer to the date.

Thanks,

Abel



From: Campbell, James R 
Sent: Wednesday, May 10, 2017 8:48 AM
To: Kho, Abel; Black, Bernard (NU); Cook, Lindsey (NU)
Cc: gpc-dev@listserv.kumc.edu
Subject: Next-D labs

Abel
It was a pleasure talking with you this morning.  I enclose a spreadsheet 
summarizing what I think was our discussion on blood sugars and appropriate 
codes for Next-D.  Please correct any misconceptions I might have included.

I checked my schedule and I have teaching responsibilities next Tuesday.  I 
would be happy to participate as much as possible by telecom if you think I 
might be helpful.  Can you forward a detailed agenda for Tuesday so that I 
might plan my time?
Jim

The information in this e-mail may be privileged and confidential, intended 
only for the use of the addressee(s) above. Any unauthorized use or disclosure 
of this information is prohibited. If you have received this e-mail by mistake, 
please delete it and immediately contact the sender.

This message and any included attachments are intended only for the addressee. 
The information contained in this message is confidential and may constitute 
proprietary or non-public information under international, federal, or state 
laws. Unauthorized forwarding, printing, copying, distribution, or use of such 
information is strictly prohibited and may be unlawful. If you are not the 
addressee, please promptly delete this message and notify the sender of the 
delivery error by e-mail.
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RE: Greetings from USC!

[Dan Connolly]

Yes, the tool is compatible with SQL Server. It originally required a lot of 
work to get python talking with SQL Server, but some sites managed that.

In recent work 
(#335), I am 
reworking the tool to use the same JDBC drivers you use to get i2b2 to talk 
with SQL Server. You might try 
seine-databuilder-0.5-3462b6609e10.zip​
 and let us know how far you get. Does the README make any sense at all? Are 
you familiar with running ant scripts as part of i2b2 installation?

The closest we come to training sessions is our weekly development call. For 
example we had some guests join us to talk about DataBuilder in our gpc-dev 31 
Jan call. We 
meet Tuesdays at 11am central. Care to suggest a Tuesday that works well for 
you? You might also flip through the SEINE DataBuilder i2b2 plugin 
Exploration
 slides and send any questions that come to mind.


p.s. Mosa, did you say you find the i2b2 workbench quite suitable for similar 
sorts of fulfillment?


--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Rekapalli, Hari 
Krishna [harikrishna.rekapa...@med.usc.edu]
Sent: Tuesday, May 09, 2017 4:09 PM
To: gpc-dev@listserv.kumc.edu
Cc: Dundon, Adam; Dirisanala, Sri Devi; Daniella Meeker
Subject: Greetings from USC!

Hi: We are considering using locally the DataBuilder tool for bidirectional ETL 
between our Redcap and i2b2 instances. Our current and a little urgent need is 
to get the data out of i2b2 system for a valid data request from a user, and 
possibly deposit that data as a CSV in an automated fashion into that user’s 
redcap account.   We have a functional i2b2 node up and running on SQL Server 
and were wondering if the tool is compatible with this DBMS. We’re presently 
using the exportXLS plugin but not too sure if this is a scalable solution for 
production environment. DataBuilder seems promising for our needs and we are 
curious to know more about. Please suggest where to start and how we can be a 
part of your training sessions.

Thanks,

Hari Krishna Rekapalli, MS, MBI
Programmer Analyst
Clinical Research Informatics
Tel: (323) 865-7654 | Email: rekap...@usc.edu


[Logomark-10%+]Translating Science into Solutions for Better Health
Southern California Clinical and Translational Science Institute (SC CTSI)
University of Southern California (USC)
SC-CTSI.org | Get Help With Your 
Research | USC 
Profiles


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RE: gpc-dev 9 May agenda and meeting notes

[Dan Connolly]

We can try, though I haven't confirmed that the folks running the meeting plan 
to attend our call.

Presuming your question is really about what is expected of UIOWA, looking at 
the Apr 25 draft agenda and 
milestone:next-d<https://informatics.gpcnetwork.org/trac/Project/milestone/next-d>,
 I don't see anything you are expected to do in preparation.


---
Dan


From: Gryzlak, Brian M [brian-gryz...@uiowa.edu]
Sent: Tuesday, May 09, 2017 8:14 AM
To: Dan Connolly; gpc-dev@listserv.kumc.edu
Cc: Al'ona Furmanchuk; charon.gladfel...@northwestern.edu
Subject: RE: gpc-dev 9 May agenda and meeting notes

Can we spend a moment on the call today to clarify what tasks participating 
NEXT-D sites are being asked to complete in advance of the meeting next week?
Brian

From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan 
Connolly
Sent: Monday, May 8, 2017 2:34 PM
To: gpc-dev@listserv.kumc.edu
Cc: Al'ona Furmanchuk <furmanc...@icnanotox.org>; 
charon.gladfel...@northwestern.edu
Subject: gpc-dev 9 May agenda and meeting notes

What else for tomorrow?

  *   gpc-dev 9 May shared 
notes<https://docs.google.com/document/d/1XtEqES6VAixHgyA_7l98semu4tvPEV7n051gYTtRsvE/edit>;
 scribe: MCRF
current snapshot with proposed agenda:




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

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

b.roll: all 12 
DevTeams<https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams> 
represented? KUMC, CMH, UIOWA, WISC, MCW MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

  i.today's scribe: MCRF

c.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)

.#596 (targeted cancer therapy study - how to fulfill feasibility data 
request?) created
<https://informatics.gpcnetwork.org/trac/Project/ticket/596>#491 (Add i2b2 
modifier for procedure source (billing, claim, etc.)) 
closed<https://informatics.gpcnetwork.org/trac/Project/ticket/491#comment:5> 
wontfix

d.Next Meeting:  16 May; scribe: UMN? WISC?

.Note LRU scribe schedule in 
#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:92>

2.
Milestone:snow-shrine-2<https://informatics.gpcnetwork.org/trac/Project/milestone/snow-shrine-2>
 due 17 May
#567<https://informatics.gpcnetwork.org/trac/Project/ticket/567> SNOW spoke 
server implementation for 
KUMC<https://informatics.gpcnetwork.org/trac/Project/ticket/567> - related 
risks...

3.
Milestone:next-d<https://informatics.gpcnetwork.org/trac/Project/milestone/next-d>
 prep for in-person meeting May 16

. #590 (next-D secure data transfer protocol) closed by gkowalski
<https://informatics.gpcnetwork.org/trac/Project/ticket/590#comment:9>Let there 
be rejoicing.

a.#444<https://informatics.gpcnetwork.org/trac/Project/ticket/444> 
pregnancy status for next-D
Mei Liu submitted GPC droc request 22 05/08/2017 2:12pm for a feasibility query 
from the 8 next-d sites.

b.#551<https://informatics.gpcnetwork.org/trac/Project/ticket/551> 
next-D labs for cohort selection: fasting glucose, HbA1c
<https://informatics.gpcnetwork.org/trac/Project/ticket/551>Dr. Campbell 
reports he and Dr. Kho have had a couple rounds of discussion and they plan to 
share their results this week.

c.#546<https://informatics.gpcnetwork.org/trac/Project/ticket/546> 
Oracle port of NextDextractionCode_12.1.16.sql
<https://informatics.gpcnetwork.org/trac/Project/ticket/546>Mei and Dan are 
working with a summer student this week.

d.#545<https://informatics.gpcnetwork.org/trac/Project/ticket/545> 
Study sample and DM sample definition for next-d
<https://informatics.gpcnetwork.org/trac/Project/ticket/545>The critical path 
looks like:

· May: test data transfer protocol 
(#590<https://informatics.gpcnetwork.org/trac/Project/ticket/590>)

· Jun: finish lab LOINC codes, SQL 
(#551<https://informatics.gpcnetwork.org/trac/Project/ticket/551>)

· Jul: integrate updated geocoding data from UMN 
(#544<https://informatics.gpcnetwork.org/trac/Project/ticket/544>)

· Aug: finish all changes to SQL code 
(#546<https://informatics.gpcnetwork.org/trac/Project/ticket/546>)

· Aug, Sep, Oct: all sites prepare, submit study sample and DM sample 
definition

4.Milestone:cdm-c2r2
<https://informatics.gpcnetwork.org/trac/Project/milestone/cdm-c2r2

gpc-dev 9 May agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 9 May shared 
notes;
 scribe: MCRF

current snapshot with proposed agenda:




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: MCRF

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

*   #596 (targeted cancer therapy study - how to fulfill feasibility 
data request?) created
#491 (Add i2b2 
modifier for procedure source (billing, claim, etc.)) 
closed 
wontfix

 *   Next Meeting:  16 May; scribe: UMN? WISC?

*   Note LRU scribe schedule in 
#12

  2.  
Milestone:snow-shrine-2
 due 17 May
#567 SNOW spoke 
server implementation for 
KUMC - related 
risks...

  3.  
Milestone:next-d
 prep for in-person meeting May 16

 *   #590 (next-D secure data transfer protocol) closed by gkowalski
Let there 
be rejoicing.

 *   #444 
pregnancy status for next-D
Mei Liu submitted GPC droc request 22 05/08/2017 2:12pm for a feasibility query 
from the 8 next-d sites.

 *   #551 
next-D labs for cohort selection: fasting glucose, HbA1c
Dr. Campbell 
reports he and Dr. Kho have had a couple rounds of discussion and they plan to 
share their results this week.

 *   #546 
Oracle port of NextDextractionCode_12.1.16.sql
Mei and Dan are 
working with a summer student this week.

 *   #545 Study 
sample and DM sample definition for next-d
The critical path 
looks like:

  *   May: test data transfer protocol 
(#590)

  *   Jun: finish lab LOINC codes, SQL 
(#551)

  *   Jul: integrate updated geocoding data from UMN 
(#544)

  *   Aug: finish all changes to SQL code 
(#546)

  *   Aug, Sep, Oct: all sites prepare, submit study sample and DM sample 
definition

  1.  Milestone:cdm-c2r2
Experience 
reports - refine GPC DevTeams Tools and 
Techniques

  2.  
Milestone:cohort-char1
 (ht/wt)
#570 collect 
expanded obesity cohort data: demographics, income, insurance / financial 
class

 *   LM / UTHSCSA will provide SQL code. And their priority (mapping) of 
financial classes

*   Done: ​Fin Class Code for 
Obesity to 
gpc-dev May 2 20:34:29

 *   GK: We did some related analysis here at MCW; I can send some details.

 *   Laura to inform Dr. Davis of risk around May 17 timeline

*   In the poll that concluded Feb 10, the PIs estimated ~6 weeks 
turn-around. May 2 + ~6 weeks = June 12. OK?

  3.  GROUSE

 *   #595 (collect i2b2 datamarts for 
GROUSE) all-sites 
please submit!




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Dan

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RE: CRG rapid cycle grants

[Dan Connolly]

Brad, you asked whether we should talk about the recent DROC request in today's 
dev call; I hadn't thought of it that way, but now that you mention it, yes, I 
suppose that's a good idea.

I added it to today's 
agenda.

Brad T., Nick, Phillip, Jim M, has the request crossed your radar? I have only 
looked at it briefly.

  *   GPC DROC Request 
21
 Use of targeted cancer therapy 04/26/2017 9:34pm (limited access)

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Phillip Reeder 
[phillip.ree...@utsouthwestern.edu]
Sent: Wednesday, April 19, 2017 12:17 PM
To: nicholas-c-sm...@uiowa.edu; Taylor, Bradley; Russ Waitman; James McClay; 
Chrischilles, Elizabeth A
Cc: Steve Fennel; gpc-dev@listserv.kumc.edu
Subject: Re: CRG rapid cycle grants

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RE: gpc-dev 2 May agenda? meeting?

[Dan Connolly]

Let's do meet and talk about how this refresh went. I'll sort of interview you 
and we can share experience.

One of the questions I'll ask is: exactly what code did you run? Would you 
please share it? So think about your answer to that in advance, please.

I might take the HackathonFour slides about each site's tools and techniques 
and refine them with some details about the CDM build process.

--
Dan


From: Dan Connolly
Sent: Monday, May 01, 2017 12:14 PM
To: gpc-dev@listserv.kumc.edu
Cc: charon.gladfel...@northwestern.edu; Al'ona Furmanchuk
Subject: gpc-dev 2 May agenda? meeting?

If anybody has made any progress that they have not shared, please do so right 
away (but not in reply to this message; send a message with an appropriate 
subject or make a comment on a relevant ticket).

I drafted a 2 May 
agenda<https://docs.google.com/document/d/1P9EBB6GObqZ39U4U0M7N9Bw-Smcr88jJ3r0JJshtL08/edit>
 based on my usual sources* but I didn't find anything to discuss other than 
perhaps pinging UMN and UTSW on 
#580<https://informatics.gpcnetwork.org/trac/Project/ticket/580> Cycle 2 
Refresh 2, and we don't really need a meeting for that.

So I'll stand by for agenda input for a bit longer and then send either a 
cancellation notice or a revised agenda.

*usual sources:

  *   stuff from last week 
(#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12>)
  *   stuff from tickets by 
milestone<https://informatics.gpcnetwork.org/trac/Project/wiki/SoftwareDev#tracking>
  *   stuff from gpc-dev 
email<https://informatics.gpcnetwork.org/trac/Project/wiki/SoftwareDev#MailingList>
  *   new/closed/reopened 
tickets<https://informatics.gpcnetwork.org/trac/Project/timeline>

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gpc-dev 2 May agenda? meeting?

[Dan Connolly]

If anybody has made any progress that they have not shared, please do so right 
away (but not in reply to this message; send a message with an appropriate 
subject or make a comment on a relevant ticket).

I drafted a 2 May 
agenda
 based on my usual sources* but I didn't find anything to discuss other than 
perhaps pinging UMN and UTSW on 
#580 Cycle 2 
Refresh 2, and we don't really need a meeting for that.

So I'll stand by for agenda input for a bit longer and then send either a 
cancellation notice or a revised agenda.

*usual sources:

  *   stuff from last week 
(#12)
  *   stuff from tickets by 
milestone
  *   stuff from gpc-dev 
email
  *   new/closed/reopened 
tickets

--
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RE: Data dictionary for obesity payer Redcap project?

[Dan Connolly]

I think the most convenient way to make a CSV file is to start with the import 
template on the the data import 
tool 
page; I just checked, and you're listed as having access to it.

If you want details about codes for radio buttons and such, try the 
codebook.

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Pedersen, Jay G 
[jay.peder...@unmc.edu]
Sent: Tuesday, April 25, 2017 4:19 PM
To: gpc-dev@listserv.kumc.edu
Subject: Data dictionary for obesity payer Redcap project?


Hi,


I have access to the GPC redcap project "Socioeconomic Variables for Obesity 
Survey"

However, I don't seem to be able to download a data dictionary related to the 
project,

so that I can create an appropriate CSV file for uploading data to the project.


I need to know how to encode race, ethnicity and financial class appropriately 
in the CSV file.

I looked at the Data Import Template ... which showed me the fields of 
interest, but not the encodings.

Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center


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RE: next-d medications issues?

[Dan Connolly]

OK. A week in advance works.

--
Dan


From: Bernard Black [bbl...@kellogg.northwestern.edu]
Sent: Tuesday, April 25, 2017 4:25 PM
To: Dan Connolly; abel@nm.org
Cc: Al'ona Furmanchuk; Charon Gladfelter; Mei Liu; gpc-dev@listserv.kumc.edu
Subject: RE: next-d medications issues?

Dan:  The May meeting will include a number of people who have not been closely 
involved with the project as of yet.
We will have a discussion, and then we will see what issues emerge . . .
We will circulate materials in advance of the meeting, but maybe a week in 
advance, not yet.  We’re not there yet.
The “definitions”, in their then current form, will be part of those materials.

Bernie

*
Bernard S. Black
bbl...@northwestern.edu
Chabraja Professor, Northwestern University
 Pritzker School of Law
 Institute for Policy Research
 Kellogg School of Management, Finance Dep’t
Law School:  375 East Chicago Ave., Chicago IL 60611
tel:  law:  312-503-2784; Kellogg:  847-491-5049; cell: 847-807-9599
papers on SSRN at:  http://ssrn.com/author=16042
*

From: Dan Connelly
Sent: Tuesday, April 25, 2017 3:35 PM
To: abel@nm.org
Cc: Al'ona Furmanchuk <furmanc...@icnanotox.org>; Charon Gladfelter 
<charon.gladfel...@northwestern.edu>; Mei Liu <mei...@kumc.edu>; Bernard Black 
<bbl...@kellogg.northwestern.edu>; gpc-dev@listserv.kumc.edu
Subject: next-d medications issues?

I see "v. Medications (Abel Kho)" on the next-d May 15-16 agenda. Are there 
issues to resolve? Are there some relevant materials to study?

I made some changes to the relevant parts of the Oracle version of the SQL 
code, but I don't believe they're substantive; I don't believe they change the 
results (though they improve performance about 6x).
(ref 
https://informatics.gpcnetwork.org/trac/Project/ticket/546#comment:13<https://urldefense.proofpoint.com/v2/url?u=https-3A__informatics.gpcnetwork.org_trac_Project_ticket_546-23comment-3A13=DwMFAw=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE=Fr9rmYHrVzv9axF0eJbDdKVFOIRmnX-4wKpzfpojMi0=t1lQSew1lcqwto-kAmYYj_g2sRcv4HEtO3opzTTtp1A=>
 Apr 5 esp. 
med_info.csv<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dckc_nextd-2Dstudy-2Dsupport_blob_master_med-5Finfo.csv=DwMFAw=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE=Fr9rmYHrVzv9axF0eJbDdKVFOIRmnX-4wKpzfpojMi0=TrCB7CvqUeelYUTcjbCW_t6K73HY-Nfcb0DA7Sx52oU=>)

I hope Alona ports this change back to the SQL Server code, but I don't suppose 
that's critical.

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RE: Overview of Data Requested - Next-D meeting prep

[Dan Connolly]

Perhaps Definitions_Part2-2017-04-19-bb.docx is actually current.

Ugh... dropbox sort by Modified doesn't work as expected. It would be more 
convenient for me if we used Dropbox's built-in version control rather than 
having separate filenames for each revision. But I gather that's not convenient 
for folks that sync with their local filesystem and want to see all the 
versions. Oh well.

Meanwhile... is there an edited change log? I could perhaps use MS Word to 
figure out what has changed, but I'm used to version control change messages 
that explain why things changed. 
https://github.com/dckc/nextd-study-support/commits/master

--
Dan



From: Dan Connolly
Sent: Tuesday, April 25, 2017 2:53 PM
To: Bernard Black
Cc: Mei Liu; charon.gladfel...@northwestern.edu; gpc-dev@listserv.kumc.edu; 
abel@nm.org; Al'ona Furmanchuk
Subject: Overview of Data Requested - Next-D meeting prep

Dr. Black,

In the NEXT-D In-Person Meeting draft agenda, I see:

 *   Overview of Data Requested (Bernie Black)

Are there any materials to study in advance? In dropbox, I see:

Definitions_Part1-2017-01-06-bb.docx (which bears 1/5/2017 at the top)
Definitions_Part2-2017-03-23-AF.docx

Are those the materials you plan to discuss?

At a high level, have things changed substantively since Dec 20? The overview 
Alona and I gave in the Dec 20 gpc-dev 
meeting<http://listserv.kumc.edu/pipermail/gpc-dev/2016q4/003463.html> was:


 *   DC and AF give an overview of NEXT-D_Request for 
Data_Detailed_12.1.16.docx<https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/539/NEXT-D_Request%20for%20Data_Detailed_12.1.16.docx>​<https://informatics.gpcnetwork.org/trac/Project/raw-attachment/ticket/539/NEXT-D_Request%20for%20Data_Detailed_12.1.16.docx>
 (attached to 
#545<https://informatics.gpcnetwork.org/trac/Project/ticket/545>): there are 
two phases of data collection:

*   Cohort definition

   *   diabetes population

   *   denominator or study population

  *   Denominator population is large: everyone with two visits

*   Follow-up observations twice per year

   *   Clinical Variables in the EMR
Details evolving in 
#539<https://informatics.gpcnetwork.org/trac/Project/ticket/539>

Supplemental Demographic Variables Returned in Geocoded Data (defined with MPC)
note #544<https://informatics.gpcnetwork.org/trac/Project/ticket/544> below
Then at the detail level: do those documents agree with 
NextDcodeForTable1_studyAndDMsampleExtraction.sql<https://github.com/dckc/nextd-study-support/blob/30506563485b2a887ae70559ac4e198127fcb5e2/NextDcodeForTable1_studyAndDMsampleExtraction.sql>
 version 3050656 
<https://github.com/dckc/nextd-study-support/commit/30506563485b2a887ae70559ac4e198127fcb5e2>
  of Apr 6?


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next-d Procedures issues?

[Dan Connolly]

I see "Procedures (Abel Kho)" on the next-d May 15-16 agenda.

Are there issues to resolve? I don't see anything about procedures in

Definitions_Part1-2017-01-06-bb.docx
Definitions_Part2-2017-03-23-AF.docx

I see "PROCEDURES" in the Apr 6 SQL 
code
 a couple times, but only for defining pregnancy events. Is there more to it?


--
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next-d medications issues?

[Dan Connolly]

I see "v. Medications (Abel Kho)" on the next-d May 15-16 agenda. Are there 
issues to resolve? Are there some relevant materials to study?

I made some changes to the relevant parts of the Oracle version of the SQL 
code, but I don't believe they're substantive; I don't believe they change the 
results (though they improve performance about 6x).
(ref https://informatics.gpcnetwork.org/trac/Project/ticket/546#comment:13 Apr 
5 esp. 
med_info.csv)

I hope Alona ports this change back to the SQL Server code, but I don't suppose 
that's critical.

--
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Overview of Data Requested - Next-D meeting prep

[Dan Connolly]

Dr. Black,

In the NEXT-D In-Person Meeting draft agenda, I see:

 *   Overview of Data Requested (Bernie Black)

Are there any materials to study in advance? In dropbox, I see:

Definitions_Part1-2017-01-06-bb.docx (which bears 1/5/2017 at the top)
Definitions_Part2-2017-03-23-AF.docx

Are those the materials you plan to discuss?

At a high level, have things changed substantively since Dec 20? The overview 
Alona and I gave in the Dec 20 gpc-dev 
meeting was:


 *   DC and AF give an overview of NEXT-D_Request for 
Data_Detailed_12.1.16.docx​
 (attached to 
#545): there are 
two phases of data collection:

*   Cohort definition

   *   diabetes population

   *   denominator or study population

  *   Denominator population is large: everyone with two visits

*   Follow-up observations twice per year

   *   Clinical Variables in the EMR
Details evolving in 
#539

Supplemental Demographic Variables Returned in Geocoded Data (defined with MPC)
note #544 below
Then at the detail level: do those documents agree with 
NextDcodeForTable1_studyAndDMsampleExtraction.sql
 version 3050656 

  of Apr 6?


--
Dan

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RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

[Dan Connolly]

Note that you're going to need a github account to write to anything that Jeff 
sets up for you; so you might as well just fork 
https://github.com/SCILHS/scilhs-ontology and add the code to your fork. If you 
want to contribute it back upstream, the norm is to do a pull request.

If you prefer to just attach a .zip file to a  message to gpc-dev, that would 
be a place to  start.

--
Dan


From: Pedersen, Jay G [jay.peder...@unmc.edu]
Sent: Monday, April 24, 2017 10:06 PM
To: Klann, Jeffrey G.; Dan Connolly
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Michael Prittie; 
Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient


Hi,


A "contrib" repo in SCILHS works for me.  It gives me a place to put this ... 
and a place for you to take a look at it, etc.

Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE  68198-5900
402-559-9487 (office)
402-739-3496 (mobile)

From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu>
Sent: Monday, April 24, 2017 9:58:00 PM
To: Pedersen, Jay G; Dan Connolly
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Michael Prittie; 
Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Might make more sense for you guys to have your own GitHub for the time being, 
and we could link to it. Or if you prefer, I’d be happy to set up a “contrib” 
repo in SCILHS that you could commit to.

Thanks,
Jeff Klann

From: "Pedersen, Jay G" <jay.peder...@unmc.edu>
Date: Monday, April 24, 2017 at 10:28 PM
To: Dan Connolly <dconno...@kumc.edu>
Cc: Hubert Hickman <huhick...@nebraskamed.com>, Russ Waitman 
<rwait...@kumc.edu>, "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>, 
Jeffrey KLANN <jeff.kl...@mgh.harvard.edu>, Michael Prittie 
<mprit...@kumc.edu>, "Campbell, James R" <campb...@unmc.edu>
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient


Hi,



I wasn't sure where to put the code in github.  I believe we are glad to share 
the code, which is written in

python and uses web services from the NLM and an input file with history 
information of RxNorm codes received from the NLM.



Where would be the appropriate spot to put that?  I thought it was supposed to 
go to the SCILHS github.


Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE  68198-5900
402-559-9487 (office)
402-739-3496 (mobile)

From: Dan Connolly <dconno...@kumc.edu>
Sent: Monday, April 24, 2017 8:56:13 PM
To: Pedersen, Jay G
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Klann, Jeffrey G.; 
Michael Prittie; Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G" <jay.peder...@unmc.edu> wrote:

Hi,



The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.



I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.



The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.



Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):



https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]



https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE  68198-5900
402-559-9487 (office)
402-739-3496 (mobile)


From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu>
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject

Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

[Dan Connolly]

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G"  wrote:

Hi,


The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.


I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.


The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.


Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE  68198-5900
402-559-9487 (office)
402-739-3496 (mobile)


From: Klann, Jeffrey G. 
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, I have not seen it either. Please point us to it, thanks.

On 4/24/17, 11:59 AM, "GPC Informatics"  wrote:

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  jay.pedersen
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics




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AdapterMappings: why 1-to-many?

[Dan Connolly]

Why do some entries in `AdapterMappings.xml` have more than one value? For 
example:



\\SHRINE\i2b2\Demographics\Age\


\\HIMC_DEMOGRAPHICS\i2b2\Demographics\Age\0-9 years old\

\\HIMC_DEMOGRAPHICS\i2b2\Demographics\Age\10-17 years 
old\

\\HIMC_DEMOGRAPHICS\i2b2\Demographics\Age\18-34 years 
old\

Doesn't it suffice to map the Age folder to the Age folder?

The only documentation I see is 
https://open.med.harvard.edu/wiki/display/SHRINE/Implementation ; is there more 
somewhere?

Are these mappings loaded into a database table? Or are they read from a file 
at run-time?

--
Dan

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gpc-dev 25 Apr agenda and meeting notes

[Dan Connolly]

What else for tomorrow? It's pretty quiet out there... :)


  *   25 Apr gpc-dev shared 
notes;
 scribe: UMN




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UMN

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

*   #594 (babel ontology update for MU) created by 
tmcneeley

*   #46 (establish gpc-dev text chat, regular discussion) 
reopened: 
The #gpc-dev IRC channel has fallen below critical mass;

*   #593 (Please load the MCW terms file into Babel) 
created

 *   Next Meeting: 2 May; scribe: UTSW? WISC?

*   Note LRU scribe schedule in 
#12

  1.  
Milestone:cdm-c2r2
 due 24 Apr

 *   #580 Data 
Characterization - Cycle 2, Refresh 2 
Tracking

*   Sites approved (yay!): UNMC, WISC, MCW, CMH

*   Submitted: KUMC, ??

*   Not submitted: ??

  2.  Milestone:adaptable-monitor
#478
 ADAPTABLE 
monitoring: Laura 
Qualls just put ADPT_AHR_WP002_NSD_B02.zip on imeet central: DRN OC 
ADAPTABLE
 folder

  3.  
Milestone:next-d
 due 9 May

  4.  
Milestone:snow-shrine-1
 due 15 May, snow-shrine-2
Due 
date revised.


--
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RE: future dates table in CDM refresh Table IIIA

[Dan Connolly]

I don't know, but the CDM folks responded right away last time I raised an 
issue in the PCORnet GitHub CDM Forum on github.

https://github.com/CDMFORUM/CDM-ERRATA/issues/19


--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Debbie Yoshihara 
[dlyos...@wisc.edu]
Sent: Monday, April 17, 2017 2:11 PM
To: gpc-dev@listserv.kumc.edu
Subject: future dates table in CDM refresh Table IIIA

Anyone know why are start and end future dates flagged for prescriptions?
I think there would be legitimate reasons why start and end future dates may 
occur for prescriptions.
Maybe for less than the 5% threshold, but nonetheless, there would be 
legitimate reasons.
We were not near the 5% threshold, but since these could be legitimate, why are 
they flagged as all?

--- Debbie Yoshihara

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gpc-dev 17 Apr agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   ​18 Apr gpc-dev shared 
notes;
 scribe: MCW




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: MCW

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

*   #582 (ADAPTABLE Phase-I Metrics) closed by 
schandaka

 *   Next Meeting: 25 Apr; scribe: UMN? WISC?

*   Note LRU scribe schedule in 
#12

  1.  
Milestone:cdm-c2r2
 due 24 Apr

 *   #580 Data 
Characterization - Cycle 2, Refresh 2 
Tracking

*   Sites approved (yay!): UNMC, WISC

*   Confirm remaining contact to submit ADD to Duke REDCap project:
UTHSCSA (C4UTHSCSA): Laura?

 *   #549 
discharge info disconnected from parts of some EI visits
Note 66afd71 and 
other recent work in cycle_2_refresh_2 branch of 
kumc-bmi/i2p-transform

 *   Any sites at-risk for 24 Apr?

  2.  
Milestone:snow-shrine-1
 due 1 May, 
snow-shrine-2

 *   #280 
Medication ontology organized by 
ingredient

*   JRC: We plan to put this on Jeff’s site (i2b2.org) and get some 
dialog from the SCILHS people on acceptability.
“Jay is pushing a copy along with documentation up to your GITHUB site for you 
and the SCILHS community to comment.” URL? commit hash?

*   #568 (Response on BABEL is painfully slow) 
reopened

*   #592 
Uploaded MCW babel terms cause db 
error

  1.  
Milestone:next-d
 due 9 May

 *   #370 (compresed file upload for use in babel DB IDE) 
reopened 
- put_terms.py is retired in favor of securefiles.kumc.edu

 *   #551 
next-D labs for cohort selection: fasting glucose, HbA1c
Note Apr 12 
revision from Dr. Kho, which presumably obsoletes the Apr 11 version that sites 
were checking earlier...

   *   UNMC: JRC comment:22:

  *   1558-6 -“OK” per Dr. Kho 12 Apr

  *   2340-8 - not in Dr. Kho’s Apr 12 revision. What to do with 
3461455 random glucose records? Current SQL code would ignore them.

   *   MCW: Kris to check MCW’s LOINC codes

   *   UTHSCSA: Laura to check

   *   UTSW:  PR: to check

  2.  babel account request for 
investigators   
Mosa, Abu S.
#260 Can't log in 
to babel rep_admin 
page - Any luck, 
Mosa?



--
Dan

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RE: UW Madison's r004 approved

[Dan Connolly]

Declaring victory in mail to gpc-dev seems to be an established pattern for 
these. It works for me. Congrats!

But if you looked for a relevant ticket in last week's call notes without 
finding one, you didn't look very hard :)

  *   #580 Data 
Characterization - Cycle 2, Refresh 2 
Tracking

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Thomas Mish 
[m...@wisc.edu]
Sent: Monday, April 17, 2017 12:01 PM
To: gpc-dev@listserv.kumc.edu
Subject: FW: UW Madison's r004 approved

Was this being tracked somewhere other than in the GPC-DEV notes? I looked at 
the latest minutes and didn’t see an obvious ticket to amend.

-TM

From: Debbie Yoshihara
Sent: Monday, April 17, 2017 11:39 AM
To: Thomas Mish ; Steger Donald A ; 
Konkol Anthony J ; UMBERTO TACHINARDI 

Subject: FW: UW Madison's r004 approved

Yay!  We did it!
That approval was fast – less than 2 hours.

 Debbie

From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Monday, April 17, 2017 11:37 AM
To: Debbie Yoshihara; Laurel Verhagen; greenlee.robert; Russ Waitman
Cc: James Topping; Laura Qualls; Darcy Louzao, Ph.D.
Subject: UW Madison's r004 approved

Good morning.

I’m happy to report that C4UWM's data characterization query response for 
refresh 4 was approved.   Please retain a static, locked copy of the SAS 
version of the characterized tables and use these data when responding to SAS 
queries issued by the DRN OC or study teams, unless instructed otherwise.  You 
may update the SAS version of all non-characterized tables and your RDBMS 
DataMart as needed.  Please contact the DRN OC if an off-cycle refresh is 
required for any of following tables: DEMOGRAPHIC, DEATH, DIAGNOSIS, 
DISPENSING, ENROLLMENT, ENCOUNTER, LAB_RESULT_CM, PRESCRIBING, PROCEDURES, and 
VITAL.

Thanks,
DRN OC Data Characterization Team
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RE: babel account request for investigators

[Dan Connolly]

Try https://babel.gpcnetwork.org/cgi-bin/babelaccess.py/rep_admin and let me 
know if it works, please?

I added you to the list of site representatives so that you can grant accounts. 
That rep_admin page was broken for a while, but I fixed it, I think.

Note that after you use the rep_admin page to create an account, you have to 
use https://babel.gpcnetwork.org/cgi-bin/babelaccess.py/password.html to get a 
password sent to the new user.

--
Dan


From: Mosa, Abu S. [mo...@health.missouri.edu]
Sent: Thursday, April 13, 2017 3:20 PM
To: gpc-dev@listserv.kumc.edu
Cc: Dan Connolly
Subject: babel account request for investigators

Hi Dan,

As part of the RFA for GPC Pilot projects, the attached documents were shared 
with the investigators. The resource guide document states that investigators 
can login to babel. What is the process for requesting babel accounts for 
investigators?

Regards,
Dr. Abu Saleh Mohammad Mosa, MS, PhD
Director, Research Informatics
University of Missouri School of Medicine
Assistant Research Professor of Health Informatics
Health Management and Informatics
One Hospital Drive, NW505, DC018.00
Columbia, MO 65212
Phone: 573-882-8349
Email: mo...@health.missouri.edu<mailto:mo...@health.missouri.edu>
Web: medicine.missouri.edu | hmi.missouri.edu




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gpc-dev 11 Apr agenda/meeting notes (incl. next-d)

[Dan Connolly]

What else for tomorrow?

  *   11 Apr gpc-dev shared 
notes
 scribe: KUMC




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: KUMC

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

*   #591 (PROCEDURES table: procedure orders? lab orders?) 
created

 *   Next Meeting: 18 Apr; scribe: UMN?
Note LRU scribe schedule in 
#12

*   Integrating hospital billing: UHC ETL 
scripts - 
standing by

  1.  
Milestone:adaptable-monitor
 due 17 Apr(?)

 *   #478 
ADAPTABLE 
monitoring draft 
adverse events query before we freeze our CDMs?

 *   Updated due date?

  2.  
Milestone:snow-shrine-1
 due 17 Apr

 *   #525 basic 
SNOW ontology alignment: Demographics, Diagnoses
JRC: to ask Jeff 
Klann why Shrine has an ontology that starts with \\SHRINE\SHRINE\Demographics 
and Pcori has \\PCORI_DEMO\PCORI\DEMOGRAPHICS

 *   Reminder to complete SNOW SHRINE 1.20.1 verification 
step!   Wanta 
Keith

 *   Shrine Terminology Files - 
Oracle   Phillip 
Reeder
Dan to send them to those who express interest (e.g. Laura @ UTHSCSA) within a 
few days

  3.  
Milestone:cdm-cycle3
 due to DRN OC 24 Apr (trac checkpoint: 17 Apr)

 *   #580 Data 
Characterization - Cycle 2, Refresh 2 
Tracking

*   Confirm remaining 7 contacts to submit ADD to Duke REDCap project: 
CMH (C4CMH), MCW (C4MCW), UIOWA (C4UI), MU (C4UMO), UNMC (C4UN), UTHSCSA 
(C4UTHSCSA), UTSW (C4UTSW)

*   #589 (principal diagnosis 10% threshold in PCORNet CDM) 
created as several 
sites are at-risk of having this issue continue beyond cycle 2 refresh 2

*   MU: plan for “ICD10 diagnosis codes do not appear to be valid 
codes”?

*   Any sites at-risk for 24 Apr?

  1.  
Milestone:next-d
 due 9 May

 *   Due date is in preparation for 16 May next-d in-person meeting

 *   #444 
Pregnancy Status for 
NEXT-D MU, can you 
try out the Apr 5 SQL Server code?

 *   #546 
Oracle port of 
NextDextractionCode_12.1.16.sql
 and factoring tabular data out of SQL code:

*   
med_info.csv
 - reduced 22 full scans of PRESCRIBING to 2

*   
lab_review.csv
 - WIP; stay tuned for update from Dr. Kho

 *   #551 
next-D labs for cohort selection: fasting glucose, 
HbA1c

*   comment:16: Apr 7 Update from GK @ MCW

   *   Next-D Glucose LOINC Code 
Analysis.xlsx​
 added by Kosinski (possible update to lab_review.csv)

*   comment:18, comment:19: “Using the CDM lab table instead 

RE: [gpc-informatics] #551: next-D labs for cohort selection: fasting glucose, HbA1c

[Dan Connolly]

I assume nearly everything is subject to change (hence careful use of version 
control). But meanwhile, I can make progress based on what I've got, so that's 
what I 'm doing.

--
Dan


From: Al'ona Furmanchuk [furmanc...@icnanotox.org]
Sent: Friday, April 07, 2017 11:37 AM
To: <gpc-dev@listserv.kumc.edu>
Cc: gkowal...@mcw.edu; Dan Connolly; Mei Liu; Taylor, Bradley; Bernard Black; 
Kho, Abel; Osinski, Kristen
Subject: Re: [gpc-informatics] #551: next-D labs for cohort selection: fasting 
glucose, HbA1c

Please, disregard Apr. 4th document on labs for now. It turned to have errors 
due to wrong application of sorting command. Earlier next week we will provide 
corrected version.

Apologies.

On Fri, Apr 7, 2017 at 11:14 AM, GPC Informatics 
<d...@madmode.com<mailto:d...@madmode.com>> wrote:
#551: next-D labs for cohort selection: fasting glucose, HbA1c
--+
 Reporter:  afurmanchuck  |   Owner:  gkowalski
 Type:  design-issue  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-stds |  Resolution:
 Keywords:|  Blocked By:
 Blocking:  545   |
--+

Comment (by dconnolly):

 George, I'm not surprised you get no results for fasting; I don't think I
 get any either. But babel shows 6777-7 is much used at MCW; that's in the
 list of codes for random glucose, yes? Do you not get any results there
 either?

 Meanwhile, note the work on `lab_review.csv` I haven't integrated it
 into the query yet; i.e. replaced the hard-coded list of LOINC codes with
 a join on a table built from `lab_review.csv`.

 Meanwhile, Dr. Kho is refining the lab spreadsheet. 5792-7 seems to be the
 most recorded glucose lab at MCW (based on c_totalnum from Babel). That
 row in Dr. Kho's Apr 4 spreadsheet says "No". I'm not sure why; he plans
 to include rationale in his next revision. 5792-7 is also not in the SQL
 code. For 6777-7, which is also much recorded, I see "allowable for now"
 and it is in the SQL code.

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/551#comment:17>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics



--
Al’ona Furmanchuk, Ph.D.
Research Associate

Center for Health Information Partnerships,
Northwestern University, Feinberg School of Medicine
633 N. Saint Clair Street, 20th floor,
Chicago, IL 60611
Web: http://furmanchuk.com/
E-mail: alona.furmanc...@northwestern.edu<mailto:furmanc...@icnanotox.org>
Phone: 312-503-34281
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SNOW SHRINE query with SCILHS PCORNet ontology (#525)

[Dan Connolly]

Keith, how is the transition from the i2b2 demo ontology to the SCILHS ontology 
going?

Any news from anybody else along these lines?

https://informatics.gpcnetwork.org/trac/Project/ticket/525

--
Dan

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RE: GPC-DEID discussion list started

[Dan Connolly]

bingo. Thanks.

-- 
Dan


From: Maren Wennberg
Sent: Thursday, March 23, 2017 1:59 PM
To: Dan Connolly; Kowalski, George; gpc-dev@listserv.kumc.edu
Subject: RE: GPC-DEID discussion list started

Hi Dan,

Please try again. You should now be able to access the archives.

Thanks,
Maren

-Original Message-
From: Dan Connolly
Sent: Thursday, March 23, 2017 1:37 PM
To: Kowalski, George <gkowal...@mcw.edu>; gpc-dev@listserv.kumc.edu; Maren 
Wennberg <mwennb...@kumc.edu>
Subject: RE: GPC-DEID discussion list started

Maren,

I just tried to access the archives but got prompted for a password. Please fix 
that. Our technical deliberations need to be open.

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Kowalski, George 
[gkowal...@mcw.edu]
Sent: Thursday, March 23, 2017 1:09 PM
To: gpc-dev@listserv.kumc.edu
Subject: GPC-DEID discussion list started

FYI ,

There is a new Text Notes De-identification discussion list we’ve started :

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

The purpose of this group is to discuss the technical aspects of the 
De-identification Software that the GPC is using.

Feel free to join if you wish to listen in on the discussion, or better yet, 
take part.

Thanks to KU and Maren for setting this up.

G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu<mailto:kosin...@mcw.edu>
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RE: GPC-DEID discussion list started

[Dan Connolly]

Maren,

I just tried to access the archives but got prompted for a password. Please fix 
that. Our technical deliberations need to be open.

-- 
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Kowalski, George 
[gkowal...@mcw.edu]
Sent: Thursday, March 23, 2017 1:09 PM
To: gpc-dev@listserv.kumc.edu
Subject: GPC-DEID discussion list started

FYI ,

There is a new Text Notes De-identification discussion list we’ve started :

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

The purpose of this group is to discuss the technical aspects of the 
De-identification Software that the GPC is using.

Feel free to join if you wish to listen in on the discussion, or better yet, 
take part.

Thanks to KU and Maren for setting this up.

G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu
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gpc-dev 21 Mar agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   ​21 Mar gpc-dev shared 
notes
 scribe: MU




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: MU

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

*   none

 *   Next Meetings:
Note LRU scribe schedule in 
#12

*   28 Mar: Dan at AMIA. Cancel? Recruit chair?

*   4 Apr scribe: UTHSCSA?

*   Integrating hospital billing: UHC ETL 
scripts - 
preferred date to discuss?

  2.  
Milestone:grouse-research-1

 *   #564 (Crosswalk files from 6 sites back from GDIT) 
closed 
fixed!
Overlap between CMS data and KUMC finder file: ~1.4M

  3.  
Milestone:cdm-cycle3
 checkpoint ~3 Apr

 *   #580 Data 
Characterization - Cycle 2, Refresh 2 
Tracking:
Here's a list of themes received by one or more sites:

1


Incorrect CDM version in HARVEST table. Update to 3.0.


WISC


2


Incorrect DATAMART_NAME in HARVEST table.


Marshfield, Regenstrief Indiana, KUMC, UTHSCSA


3


the % of encounters without a principal diagnosis was calculated incorrectly in 
the EDC report/will be below 10% threshold.


Marshfield, UNMC, Regenstrief Indiana, UTHSCSA


4


Future Dates - enrollment end date (July 2016) after refresh date (June 2016)


Iowa


5


ICD9 diagnosis codes do not appear to be valid codes


KUMC


6


ICD10 diagnosis codes do not appear to be valid codes


Regenstrief/Indiana?,
 UTHSCSA (100%), Either Missouri or Minnesota (message sent to T.Meyer, but 
datamart referenced was C4UMO not C4UMA)


7


Data coded as ICD9 after the ICD9/10 transition dates in the Diagnosis and 
Procedures tables.


Iowa


8


Orphan Encounter IDs - if the encounter appears on a data record, it's expected 
to exist in the Encounter table


Iowa


9


Dispensing records in DataMart_All, but nothing in Dispensing DC


Iowa



 *   CDM V3.X PROCEDURES
JRC: during 
DRNOC discussions, it became clear that how the procedures tables is populated 
varies widely between datamarts - 12x in some cases.
Labs were deemed relevant to be coded as procedures.  What is appropriate for 
GPC to fall under the procedure tables?
Discussion continued after the scheduled time; it wasn’t entirely conclusive.

 *   interoperable procedure order ontology by looking at link between 
orders and billing 
transactions?  
Russ Waitman

  1.  
Milestone:snow-shrine-1
 due 20 Mar

 *   #460 SNOW 
SHRINE node at UTSW
SNOW Shrine 
Ontologies   
Phillip Reeder Thu Mar 9

 *   Update shrine-1 milestone ETA? I.e. leading sites (WISC, UTSW, MCRF, 
IU) operational

  2.  
Milestone:snow-shrine-2
 due ~Apr

 *   #280, 
MEDICATIONS metadata for SCILHS

*   UNMC will install SCILHS metadata into Babel.

*   Note Russ/KUMC March 15 feedback 
comment:16

*   JRC to solicit input Marsolo and company from the national 
antibiotics study
https://github.com/CDMFORUM/CDM-GUIDANCE/issues

*   Tom/Debbie/WISC 
review

 *   Status at shrine-2 sites:

*   KUMC 
#567: we’re 

RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

[Dan Connolly]

As to who is going to look at them: i2p-transform (i.e. software to build 
PCORNet CDM from i2b2) consumes these modifiers.

As to 11x: how many modifiers are you currently storing? You're already storing 
RX_BASIS, RX_FREQUENCY, RX_DAYS_SUPPLY, RX_QUANTITY, and RX_REFILLS somehow, 
yes?

UNMC was proposing adding RX_STRENGTH, RX_ROUSE, RX_DOSE, and RX_SIG, but in 
discussion it emerged that "justification for including route, dose and detail 
modifiers ... is weakest in terms of use cases"

I count 9 total modifiers in the proposal, 5 of which KUMC (and presumably the 
other 8 sites using the i2p-transform code) are already loading, and 3 of which 
could (from discussion so far) be removed without much objection. So to me, it 
looks like this is a proposal to go from 5 to 6 modifiers.

-- 
Dan


From: Debbie Yoshihara [dlyos...@wisc.edu]
Sent: Monday, March 20, 2017 10:09 AM
To: gpc-dev@listserv.kumc.edu; Thomas Mish; campb...@unmc.edu; 
huhick...@nebraskamed.com; Dan Connolly; Russ Waitman
Cc: jeff.kl...@mgh.harvard.edu
Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

I have looked over these explosion of modifiers.
For the med modifiers if you populated all of them that would make the facts 
11x bigger for the med facts.
Who is going to look at all of these? Or even populate them if they have them?

The only other question I have is for the lab_mod, what is the difference 
between stat and expedite?

--- Debbie Yoshihara



-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC 
Informatics
Sent: Monday, March 20, 2017 8:46 AM
To: Thomas Mish; campb...@unmc.edu; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  mish
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+
Changes (by dconnolly):

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/280#comment:17>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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gpc-dev 14 March agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   ​14 Mar gpc-dev shared 
notes;
 scribe: IU




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW 
(regrets Reeder), MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: IU

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

*   #354 (First wave of recruiting ADAPTABLE patients) 
closed 
fixed

*   #587 (SNOW SHRINE spoke install at UNMC) 
 created; 
closed duplicate

 *   Next Meetings: 21 Mar: scribe: MU?
Note LRU schedule in 
#12

*   #460 
Reeder would like “to discuss and show the SNOW Shrine with the SCIHLS 
ontologies” 21 Mar

*   Integrating hospital billing: UHC ETL 
scripts - 
preferred date to discuss?

  2.  
Milestone:cohort-char-bc-db
 due 13 Mar

 *   #297 (collect breast cancer data from GPC sites for linking with 
surveys, ...) 
closed 
fixed

 *   #584 
Possible blended registry 
record (WISC) - 
REDCap updated?

  3.  
Milestone:snow-shrine-1
 due 13 Mar

 *   #460 SNOW 
SHRINE node at UTSW 
next week. regrets Reeder

 *   #459 MCRF 
experience with SHRINE on Microsoft platform

 *   #531 SNOW 
SHRINE node at MCRF with SCILHS PCORnet 
ontology

 *   #575 SNOW 
SHRINE 1.20.1 install for 
IU

  4.  
Milestone:snow-shrine-2
 due ~Apr

 *   #280, 
MEDICATIONS metadata for SCILHS
“waiting for responses from GPC.” but ticket is still assigned to jay.pedersen 
- recruit >= 2 reviewers.

  5.  
Milestone:cdm-cycle3
 checkpoint ~3 Apr

 *   #580 Data 
Characterization - Cycle 2, Refresh 2 
Tracking - review 
status

 *   #579 Data 
Characterization - Cycle 3 
Tracking - review 
status

 *   #549 
discharge info disconnected from parts of some EI 
visits

 *   CDM V3.X 
PROCEDURES

  6.  
Milestone:cohort-char1
 due 17 Apr?

 *   #570 - IRB 
update on track for ~1 month after 13 Feb?
1 month has come and gone. So 17 Apr is at-risk.




--
Dan

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RE: CDM V3.X procedures (was: #583: SNOW SCILHS Lab Metadata Expansion)

[Dan Connolly]

Jim and everybody,

It would help me if you could give one or two specific examples of each of 
these:
 - Clinic and hospital E and professional procedures with CPT coding

Am I missing something there? Isn't this the ordinary CPT code stuff we already 
do?
This is already in EDC tables and charts, yes?

 - Clinic and hospital surgery and other diagnostic and therapeutic
   procedures with ICD-10-PCS coding

Likewise, this doesn't look new to me.

 - Laboratory orders (with LOINC or CPT coding)

LOINC isn't new is it? Oh... orders, not results. OK. That would be tricky. We 
have lots of lab order data, but it's all in local coding.

 - Medications administered (clinic or hospital) with NDC coding

I have never seen NDC codes for medications adminstered in the KU Epic system.

-- 
Dan


From: GPC Informatics [d...@madmode.com]
Sent: Sunday, March 12, 2017 5:02 PM
To: campb...@unmc.edu; Dan Connolly
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #583: SNOW SCILHS Lab Metadata Expansion

#583: SNOW SCILHS Lab Metadata Expansion
---+---
 Reporter:  campbell   |   Owner:  campbell
 Type:  enhancement|  Status:  assigned
 Priority:  major  |   Milestone:  snow-
Component:  data-stds  |  shrine-2
 Keywords:  LOINC Lab_PRO_CM SCILHS all-sites  |  Resolution:
 Blocking: |  Blocked By:
---+---

Comment (by campbell):

 Data characterization calls the past 3-4 weeks with DRN OC have indicated
 that CDM V3.X PROCEDURES should support when available:
 Clinic and hospital E and professional procedures with CPT coding
 Clinic and hospital surgery and other diagnostic and therapeutic
 procedures with ICD-10-PCS coding
 Laboratory orders (with LOINC or CPT coding)

 May support when available:
 Medications administered (clinic or hospital) with NDC coding

 If we agree as a network we want to comply and we want this data in SNOW
 SHRINE and have standard extracts to CDM PROCEDURES, then we need to agree
 on SCILHS modifier extensions for medication administration and for orders

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/583#comment:5>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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gpc-dev 7 Mar agenda and meeting notes

[Dan Connolly]

Anything else for tomorrow?

  *   ​gpc-dev 7 Mar shared 
notes
 scribe: UNMC




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UNMC

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

*   #563 (Finder File for GROUSE(UMN)) 
closed 
wontfix

 *   Next Meetings: 14 Mar: scribe: MU? IU?
Note LRU schedule in 
#12

*   Integrating hospital billing: UHC ETL 
scripts - 
preferred date?

  2.  
Milestone:cohort-char-bc-db
 due 6 Mar

 *   #466 (duplicate tumor records: same subject, sequence number) closed 
 fixed

 *   #538 (medications by VA class not available from MCW) 
closed 
wontfix

 *   #584 
Possible blended registry 
record (WISC)

  3.  
Milestone:snow-shrine-2
 due ~Apr

 *   #583 SNOW 
SCILHS Lab Metadata 
Expansion - 
timeframe for sites to reply?

 *   #586 SNOW 
SHRINE node at CMH with SCILHS PCORnet 
ontology - on track 
for Apr?

  4.  
Milestone:cohort-char1
 due 17 Apr

 *   #570 - IRB 
update on track for ~1 month after 13 Feb?
Ticket #570 - insurer 
question   
Gardner, Bret J


--
Dan

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RE: Share CDM Data Characterization (EDC) report with GPC customers such as Next-D

[Dan Connolly]

We're down to two bottle of beer on the wall: WISC, UTHSCSA.

Pretty please?

--
Dan


From: Dan Connolly
Sent: Monday, February 27, 2017 11:37 AM
To: <gpc-dev@listserv.kumc.edu>
Subject: RE: Share CDM Data Characterization (EDC) report with GPC customers 
such as Next-D

Thanks, Rita, for submitting CMH's EDC report.

We're down to 3 remaining sites: UTHSCSA, WISC, MCRF.

Are there any barriers I can remove?

--
Dan


From: Dan Connolly
Sent: Tuesday, January 24, 2017 1:32 PM
To: <gpc-dev@listserv.kumc.edu>
Cc: Mei Liu
Subject: Share CDM Data Characterization (EDC) report with GPC customers such 
as Next-D

Please use this redcap survey to submit them:
https://redcap.gpcnetwork.org/surveys/?s=9LT4KE8NFD

We are collecting EDC reports from GPC sites to share with prospective GPC 
customers; for example, the Next-D researchers.

These reports will not be shared publicly.

For context, see #571 characterization of data from next-d GPC 
sites<https://informatics.gpcnetwork.org/trac/Project/ticket/571>.
--
Dan

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gpc-dev 28 Feb agenda and meeting notes

[Dan Connolly]

What else for 
tomorrow?

  *   gpc-dev 28 Feb shared meeting 
notes;
 scribe: CMH

current snapshot with proposed agenda:



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

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

 *   roll: all 12 
DevTeams 
represented? KUMC (regrets: McMahon), CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, 
UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: CMH

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

*   #585 (Create GPC ontology for SNOW SHRINE network) 
 created, 
closed invalid

*   #273 (ADAPTABLE study ID linkage, REDCap 
integration)
 re-opened, closed (see #541 for follow-up)

*   #417 (Submit Progress Report on enhancement of obesity cohort 
(milestone 
2.11.3)) 
closed (for this reporting period), reopened (for six months from now)

 *   Next Meetings: 28 Feb: scribe: MU? UNMC?
Note LRU schedule in 
#12

  2.  
Milestone:cohort-char-bc-db
 due 27 Feb

 *   #466 
duplicate tumor 
records in MCW data 
ETA 27 Feb

 *   #584 
Possible blended registry 
record (MCW)

  3.  
Milestone:grouse-research-1
 due 28 Feb

 *   #559 Finder File for GROUSE(UIowa) 
closed 
Feb 20

 *   #540 
Finder file for GROUSE 
(UTHSCSA)

 *   #557 
Finder File for 
GROUSE(IU)

 *   #563 
Finder File for 
GROUSE(UMN)

  4.  
Milestone:snow-shrine-1
 “4 weeks” arrives 6 Mar

 *   #532 UNMC: 
21 Feb update: “Nebraska has received authorization from our security team and 
we are proceeding with installation of SNOW SHRINE software node on open 
internet”

 *   News from MCRF 
(#531), IU 
(#575), UTSW 
(#460) or others?

 *   #459 How 
to add GPC sites to SNOW SHRINE network?
MCRF to report 
experience installing on SQL Server and Windows.
Still relevant?

 *   #583 SNOW 
SCILHS Lab Metadata 
Expansion - 
timeframe for sites to reply?

  5.  
Milestone:next-d
 due ~6 Mar

 *   #551 
next-D labs for cohort selection: fasting glucose, 
HbA1c  - progress 
at MCW?

  6.  Share CDM Data Characterization (EDC) report with GPC customers such as 
Next-D 24 Jan
Survey: https://redcap.gpcnetwork.org/surveys/?s=9LT4KE8NFD

 *   Received from all 8 nextD sites + CMH; we would like them from the 
remaining 3 sites (UTHSCSA, WISC, MCRF)

  7.  Integrating hospital billing: UHC ETL 
scripts

  8.  

RE: Ticket #570 - insurer question

[Dan Connolly]

Dean, suggestions? (you own #570)

--
Dan


From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Gardner, Bret J 
[bret.gard...@unmc.edu]
Sent: Wednesday, February 22, 2017 10:58 AM
To: gpc-dev@listserv.kumc.edu
Subject: Ticket #570 - insurer question

I am working to get insurer information for the obesity study cohort.  I have 
located the necessary information in Epic, however, some patients have multiple 
financial classes listed.  I am wondering how this multiplicity should be 
resolved.  Should we send a list with patient_nums and all financial classes 
they have listed, or, is there an approach to limit the list so a single 
patient has a single financial class.
Thank you,

Bret J. Gardner
Graduate Student
University of Nebraska Medical Center
MD/PhD Scholars Program
bret.gard...@unmc.edu
801-455-5168 (cell)


The information in this e-mail may be privileged and confidential, intended 
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RE: Share CDM Data Characterization (EDC) report with GPC customers such as Next-D

[Dan Connolly]

Thanks, Rita, for submitting CMH's EDC report.

We're down to 3 remaining sites: UTHSCSA, WISC, MCRF.

Are there any barriers I can remove?

--
Dan


From: Dan Connolly
Sent: Tuesday, January 24, 2017 1:32 PM
To: <gpc-dev@listserv.kumc.edu>
Cc: Mei Liu
Subject: Share CDM Data Characterization (EDC) report with GPC customers such 
as Next-D

Please use this redcap survey to submit them:
https://redcap.gpcnetwork.org/surveys/?s=9LT4KE8NFD

We are collecting EDC reports from GPC sites to share with prospective GPC 
customers; for example, the Next-D researchers.

These reports will not be shared publicly.

For context, see #571 characterization of data from next-d GPC 
sites<https://informatics.gpcnetwork.org/trac/Project/ticket/571>.
--
Dan

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gpc-dev 21 Feb agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 21 Feb shared meeting 
notes;
 scribe: UIOWA




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UIOWA

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

*   none

 *   Next Meetings: 28 Feb: scribe: WISC? CMH?
Note LRU schedule in 
#12

*   Integrating hospital billing: UHC ETL 
scripts - good 
time to discuss?

  2.  Share CDM Data Characterization (EDC) report with GPC customers such as 
Next-D 24 Jan
Non NEXT-D sites are invited to participate: CMH, WISC, MCRF, UTHSCSA
Survey: https://redcap.gpcnetwork.org/surveys/?s=9LT4KE8NFD

  3.  #335 
DataBuilder update: “Bill Riedl of U.C. Davis has worked through the kinks for 
delivery to REDCap using the all-JVM branch”
seine-databuilder-0.5-6402ad53491f.zip​
 (8.1 MB)

  4.  
Milestone:gpc-phase2-h4
 due 31 Jul
#431 text notes - 
Jay Urbain of MSOE to join

 *   #572 
enterprise scale unstructured text notes de-identified, in 
i2b2

 *   #573 
de-identified text notes for on a cohort-by-cohort 
basis



--
Dan

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gpc-dev 14 Feb agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 14 Feb shared 
notes;
 scribe: MCW

current snapshot with proposed agenda:




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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: MCW

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

*   #263 (Adaptable cohort query design and administration) 
closed

*   #582 (ADAPTABLE Phase-I Metrics) 
created

*   #581 (Crosswalk files for the remaining 5 GPC sites back from GDIT) 
created

 *   Next Meetings:

*   21 Feb: scribe: UIOWA?
Note LRU schedule in 
#12

*   21 Feb - 
#431 text notes - 
Jay Urbain of MSOE to join

  2.  
Milestone:cohort-char-bc-db
 due 13 Feb

 *   #466 
duplicate tumor 
records in MCW data

 *   #566 
medication exposure missing from UIOWA breast cancer 
submission

  3.  
Milestone:grouse-research-1
 due 28 Feb

 *   WISC #562 
done

 *   Not done? UTHSCSA 
#540, IU 
#557, UIOWA 
#559, UMN 
#563

  4.  Integrating hospital billing: UHC ETL 
scripts

  5.  
Milestone:next-d
 due 6 March (?)

 *   #571 
characterization of data from next-d GPC 
sites: done: “All 8 
participating GPC sites have uploaded their EDC reports and Mei has sent them 
to Alona at Northwestern.”

 *   #551 
next-D labs for cohort selection: fasting glucose, 
HbA1c “George and 
Brad, do you think the approach Dan proposed in 
comment:8 
is reasonable for other GPC sites?”

  6.  
Milestone:snow-shrine-1
 ETA 6 Mar, 
snow-shrine-2

 *   Phillip - yes; I can clarify what I’m saying about mappings in email.
Still relevant? overtaken?

 *   #575 IU: 
Dan H. will provide an estimate. Done: “... 4-5 weeks …”

 *   #583 SNOW 
SCILHS Lab Metadata 
Expansion

  7.  
Milestone:cdm-cycle3
 checkpoint 3 Apr

 *   #580 Data 
Characterization - Cycle 2, Refresh 2 
Tracking - “Query 
Distribution: 4/1/17”

 *   #578 DC 
Cycle 3 - Beta 
Testing “Marshfield 
is willing to volunteer to take the beta testing role.”

 *   #579 Data 
Characterization - Cycle 3 
Tracking

  8.  

RE: [SCILHS/scilhs-ontology] Medication ontology: SHRINE interop below ingredient level? (#52)

[Dan Connolly]

Good question, Lori. I hope to reply in substance in the next week or two. If 
you haven't heard from me/us in that timeframe, please remind us.

Jim C., Nathan, Phillip, Russ, and everybody, please consider Lori's question.

It's relevant to at least a couple of our issues:

Medication ontology orgainzed by 
ingredient<https://informatics.gpcnetwork.org/trac/Project/ticket/280>
https://informatics.gpcnetwork.org/trac/Project/ticket/280


Shared GPC medication hierarchy after NDF-RT ceases publication by Q1 
2017<https://informatics.gpcnetwork.org/trac/Project/ticket/519>
https://informatics.gpcnetwork.org/trac/Project/ticket/519

Lori's quote of me comes from 
https://github.com/SCILHS/scilhs-ontology/issues/52

--
Dan


From: Phillips, Lori C. [lcphill...@partners.org]
Sent: Tuesday, February 07, 2017 9:06 AM
To: Dan Connolly
Subject: RE: [SCILHS/scilhs-ontology] Medication ontology: SHRINE interop below 
ingredient level? (#52)

Dan,

“SCDs and SBDs with significant usage are obsoleted remarkably often. (IOU an 
example or two.)”

Is it the codes that are deprecated or the medications themselves?

i.e. does a given medication get assigned a new code?

Also, the medications that you get from your EMRs … do they have rxnorm codes 
or are they something else that is mapped to rxnorm?

Thanks
Lori

From: Dan Connolly [mailto:notificati...@github.com]
Sent: Tuesday, February 07, 2017 9:52 AM
To: SCILHS/scilhs-ontology <scilhs-ontol...@noreply.github.com>
Cc: Phillips, Lori C. <lcphill...@partners.org>; Mention 
<ment...@noreply.github.com>
Subject: Re: [SCILHS/scilhs-ontology] Medication ontology: SHRINE interop below 
ingredient level? (#52)


"for SHRINE probably ingredient would be ok" addresses my question; as it 
appears we are agreed, I'm closing this. Feel free to re-open to reconsider, of 
course.

As to the rest...

Our original concern was that we compared KUMC's RXNORM organization with this 
one and we didn't see much of a pattern in the relationship. Perhaps when we 
re-organize around ingredient, we will find that we have the same set of SCDs 
and SBDs below each ingredient, but it seems unlikely.

Also, RxNorm is updated weekly, and the updates are evidently not just fringe 
things that have no intersection with the bulk of usage. SCDs and SBDs with 
significant usage are obsoleted remarkably often. (IOU an example or two.)

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on 
GitHub<https://github.com/SCILHS/scilhs-ontology/issues/52#issuecomment-278022087>,
 or mute the 
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The information in this e-mail is intended only for the person to whom it is
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Integrating hospital billing: UHC ETL scripts

[Dan Connolly]

Brad,

You and the MCW folks have expressed interest in using KUMC's UHC ETL scripts 
to integrate hospital billing. Please spend a few minutes poking around our 
documentation and / or code and reply with any questions that come to mind.

https://informatics.kumc.edu/work/wiki/UHCSource

https://github.com/kumc-bmi/heron/blob/master/heron_load/uhc_concepts_load.sql

The Feb 14 gpc-dev weekly call looks like a good time to discuss this in 
detail, but as usual, the more preparation we can do outside the meeting, the 
better chance we have of making good use of the meeting time.

Here are a couple questions to prime the pump:

Sketch your use case? i.e. tell me a story about what you imagine it looks like 
when it's all set up and working at your site. Is this intended to address 
issues that show up in your CDM EDC report? If so, which charts / tables 
specifically?

If somebody like George can take a look and imagine yourself following our 
documentation, what's the first place where the next step is not clear?

--
Dan

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gpc-dev 7 Feb agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   gpc-dev 7 Feb shared meeting 
notes;
 scribe: UTSW

current snapshot with proposed agenda:



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

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

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: UTSW

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

*   #528 (Documentation of UNMC i2b2 ETLs for Epic) closed by 
jmcclay

*   #548 
how to set up MyChart for ADAPTABLE 
recruitment? closed

 *   Next Meetings:

*   14 Feb: scribe: MCW?
Note LRU 
schedule

*   21 Feb - 
#431 text notes - 
Jay Urbain of MSOE to join

  2.  
Milestone:cohort-char-bc-db
 due 6 Feb

 *   #482 (MCW missing surgery and examined nodes in breast cancer 
DataBuilder file) 
closed

 *   #466 
duplicate tumor 
records in MCW 
data: “several pairs of records with the same study id and date of diagnosis, 
one with sequence :00 and one with :XX”

 *   #566 
medication exposure missing from UIOWA breast cancer 
submission

  3.  
Milestone:snow-shrine-1
 checkpoint 6 Feb

 *   #531 SNOW 
SHRINE node at MCRF with SCILHS PCORnet 
ontology

 *   #575 SNOW 
SHRINE 1.20.1 install for 
IU

 *   Quick screen-share show-and-tell.

 *   estimate when we'll have some basic queries working at a handful of 
sites - the leading sites seem to be MCRF, UTSW, and IU (along with WISC)

 *   aiming for April for milestone:snow-shrine-2

  4.  
Milestone:cohort-char1
 (obesity) requested by 17 Feb

 *   #570 
collect expanded obesity cohort data: demographics, income, insurance / 
financial class: 
“The effort, regulatory issues, and deadline for this task were discussed in 
the 1 Feb GPC Governance Council. The outcome was a ​poll on feasibility and 
schedule. Responses are 
requested from all GPC sites by 6 Feb.”

  5.  
Milestone:grouse-research-1
 due 28 Feb

 *   #564 
Crosswalk files from 6 sites back from GDIT
Done: KUMC, MCRF, 
MU, UNMC, UTSW, MCW

 *   Not done? UTHSCSA 
#540, IU 
#557, WISC 
#562, UIOWA 
#559, UMN 
#563

*   Technical questions?

*   Advice wanted on where to direct regulatory questions?

*   Stay tuned for info from Steve Fennel on budget impact.

  6.  
Milestone:adaptable-accrual
 due 1 Mar
#354 First wave of 
recruiting ADAPTABLE 
patients comment:16:

 *   UTSW is waiting 

SNOW SHRINE update?

[Dan Connolly]

Keith, thanks for the updates.

If anyone has news they have not shared, please do so.

  *   
ticket:531#comment:5
 31 Jan update on testing the MCRF node: "... the hub did not trust the spoke 
..."
  *   
ticket:575#comment:3
 Feb 1 update on IU spoke: "... inbound and outbound TCP SSL traffic is working 
as expected for the IU spokes ..."

Since estimating "one or two weeks" at HackathonFour to get certificate 
exchange done, we've learned of various other complications. Given what we know 
now, I'd like us to come up with a new 
snow-shrine-1
 estimate when we'll have some basic queries working at a handful of sites - 
the leading sites seem to be MCRF, UTSW, and IU (along with WISC).

By the way... if there are any queries working at WISC, perhaps you could share 
one or two of them? (print query, XML form.) ref 
#525

Though the news won't likely be all good, it does look like a quick 
show-and-tell in tomorrow's call will be worthwhile. I wouldn't mind a replay 
of the status of errors at MCRF or a peek at what happens if we try at IU.


--
Dan

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