Re: [gpc-informatics] #473: PCORnet CDMv3 SAS Readiness

2016-02-09 Thread GPC Informatics 
#473: PCORnet CDMv3 SAS Readiness
---+
 Reporter:  lv |   Owner:  lv
 Type:  task   |  Status:  assigned
 Priority:  major  |   Milestone:  gpc-phase2-h1
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:
 Blocking: |
---+

Old description:

> ''Laurel reporting on behalf of Darcy Louzao:''
>
> Specifically, can you verify/update the date at which each data partner
> will be ready to receive the Diagnostic Query (DQ), for which the
> requirements are:
>
> • CDM v3.0 with SAS data types
> • All 15 tables present
> • Demographic, Enrollment, Encounter, Diagnosis, Procedures, Vital, and
> Harvest tables populated
>
> ||Site  ||SAS CDM v3 Readiness Date/DQ Status
> ||Children's Mercy  ||TBD
> ||Indiana U Regenstrief ||3/1/16
> ||Marshfield Clinic ||Completed DQ
> ||Med Coll Wisconsin||3/31/16
> ||U of Minnesota AHC||3/31/16
> ||U of Missouri HC  ||6/30/16
> ||U of Nebraska ||3/15/16
> ||University of Iowa||TBD
> ||University of Kansas  ||DQ sent 2/2/16
> ||UT San Antonio||DQ sent 2/2/16
> ||UT SW Med Ctr ||DQ sent 2/2/16
> ||UW Madison||3/14/16
>

>
> Additionally, please keep the following points in mind for future
> planning:
> 1. We will send the Diagnostic Query based on the dates you provide (I
> will check-in the week prior to sending to verify readiness)
> 2. We will request a response in ~2 weeks
> 3. Requirements for the next step, Data Characterization, are:
> • Successful diagnostic response, ie. no exceptions noted (in the
> workplan they are described as “unexpected conditions”)
> • Locked/static data
> • Will need to submit an ETL ADD with their query response (the template
> is on our Data Characterization wiki)

New description:

 ''Laurel reporting on behalf of Darcy Louzao:''

 Specifically, can you verify/update the date at which each data partner
 will be ready to receive the Diagnostic Query (DQ), for which the
 requirements are:

 • CDM v3.0 with SAS data types
 • All 15 tables present
 • Demographic, Enrollment, Encounter, Diagnosis, Procedures, Vital, and
 Harvest tables populated

 ||Site  ||SAS CDM v3 Readiness Date/DQ Status
 ||Children's Mercy  ||06/15/16
 ||Indiana U Regenstrief ||03/01/16
 ||Marshfield Clinic ||Completed DQ
 ||Med Coll Wisconsin||03/31/16
 ||U of Minnesota AHC||03/31/16
 ||U of Missouri HC  ||06/30/16
 ||U of Nebraska ||3/15/16
 ||University of Iowa||TBD
 ||University of Kansas  ||DQ sent 2/2/16
 ||UT San Antonio||DQ sent 2/2/16
 ||UT SW Med Ctr ||DQ sent 2/2/16
 ||UW Madison||03/14/16



 Additionally, please keep the following points in mind for future
 planning:
 1. We will send the Diagnostic Query based on the dates you provide (I
 will check-in the week prior to sending to verify readiness)
 2. We will request a response in ~2 weeks
 3. Requirements for the next step, Data Characterization, are:
 • Successful diagnostic response, ie. no exceptions noted (in the workplan
 they are described as “unexpected conditions”)
 • Locked/static data
 • Will need to submit an ETL ADD with their query response (the template
 is on our Data Characterization wiki)

--

Comment (by lv):

 Updating with date for CMH.

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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Re: gpc-dev agenda and meeting notes for Feb 9 11am

2016-02-09 Thread Phillip Reeder 
Looking at the gpc lab terminology, it looks like we are missing lab units in 
the metadata.  Does anyone have a complete set of lab metadata with units?

Phillip

From: Dan Connolly >
Date: Monday, February 8, 2016 at 3:53 PM
To: "gpc-dev@listserv.kumc.edu" 
>
Subject: gpc-dev agenda and meeting notes for Feb 9 11am

What else for tomorrow? Scribe volunteers are welcome.

  *   9 Feb 2016 GPC-Dev meeting 
notes

Current proposal:



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

 *   ​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

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

*   today's scribe: IU ??

*   reminders from current work by owner 
site:

 *   comments on the agenda? on last week’s notes 
(#12)? recent 
tickets opened/closed 
FYI (note also recent ticket comments 
report):

   *   #451 (X02 Application - NIH CTSA for Collaborative Innovation 
(Barohn PI)) 
closed

   *   #472 (Assess quality and quantity of Wisconsin Medicaid data) 
created - owner: 
btaylor
#93 (federated login for GPC services such as babel) 
reopened

   *   #398 (next-d post-award processes) 
closed

   *   #399 (WISC ALS survey on regulatory stand-by) 
closed

 *   Next Meeting: 16 Feb Scribe: LRU nominates IU, MU, UNMC, UTSW, 
etc.

  2.  
milestone:data-quality-q3
 - Feb 15

 *   
depgraph

 *   alternative: PCORnet CDM

 *   alternative: OHDSI tools

  3.  
milestone:gpc-phase2-h1
 Feb 22

 *   CDM v3 - DRN OC 
timeline

 *   #473 PCORnet CDMv3 SAS Readiness - poll by site (see 
below)

*   #117 (SAS miniSentinel environment for the PCORNet DRN queries) 
closed 
as dup

 *   #465 (date obfuscation (shifting) for PCORnet CDM queries) closed
Somebody 
asked about this at the hackathon. Here’s your answer: “Per Russ in GPC PMO, 
closing until we see national governance around data.
PerGPC 
DSA
 have allowances to run queries around de-identified dates.”

  4.  next QA milestone

 *   reproducible CDM refresh 
#160

 *   SHRINE / SNOW - 
#459 docs

  5.  
milestone:adaptable-accrual
 Feb 29

 *   FW: PCORnet ADAPTABLE data strategy 
discussion  
Shelley Rusincovitch

*   slides, code, discussion 
thread

*   Did anyone attend? If so, debrief.

  6.  
milestone:cohort-char1
 March 15

 *   #458sqlite 
validation tool for Weight and Health 
survey - done.
#379Link EHR data 
to Health and Medical Research Family Survey (HMRFS) 2 results
poll by phase 1 
site for validation results,

FW: ADAPTABLE First 100

2016-02-09 Thread Russ Waitman 
Hi All,
Just a heads up that ADAPTABLE is moving forward.  Iowa IRB is close to 
completing their review as well.  Exciting times….

Russ


From: Adrian Hernandez, M.D. [mailto:adrian.hernan...@duke.edu]
Sent: Monday, February 08, 2016 12:17 PM
To: Thomas Carton; Russell Rothman; McTigue, Kathleen; Rachel Hess; Rainu 
Kaushal; Lucila Ohno-Machado; Russ Waitman; Terry Mazany; Gary E Rosenthal
Subject: ADAPTABLE First 100

All

In the next day, all the CDRNs participating in ADAPTABLE should receive their 
final packets for IRB approval for the ADAPTABLE trial.  While its been a 
longer road to get here than expected but I’m hopeful that the upfront 
investment in time/energy that has been placed will pay off dividends.

To that end, we are going to really need your help, as CDRN leaders, and 
feedback to push forward the final administrative hurdles for getting ADAPTABLE 
launched.  Please let me know about any issues you hear about with either 
contracting or IRB.  We’re going to pushing out information to you all 
regarding where things stand so we can learn from each other.

In addition, there is a ton of interest in the early success of the ADAPTABLE 
trial from multiple external stakeholders (NIH, FDA, Industry) and specifically 
regarding the approach towards creating a National Evidence Generation System.  
PCORNet and ADAPTABLE will be specifically highlighted in an upcoming public 
workshop (Enhancing the Application of Real-World Evidence in Regulatory 
Decision Making) scheduled for March 3/4 in DC.  Interested parties will want 
to see how PCORnet is able to deliver pragmatic randomized clinical trials at a 
scale that incorporates 
e-approach/e-engagement/e-consent/e-randomization/e-follow-up.

In this regard, we are encouraging everyone to consider approach and time to 
get to first 100 patients for each CDRN ala PCORnet style.  Typically, we 
consider time to first patient in (FPI) or last patient out (LPO) as metrics of 
success but of course the interest for PCORnet is to do things @ 10X!


Best
Adrian
__
Adrian F. Hernandez, MD, MHS
Director, Health Services and Outcomes Research
Faculty Associate Director
Duke Clinical Research Institute
PO Box 17969
Durham, NC 27715
Phone 919-668-7515
Mobile 919-812-3463
Fax 919-668-7058

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Re: [gpc-informatics] #327: Gather 2015 4th quarterly QA results (and 3rd quarter if feasible) (was: Gather 2015 3rd, 4th quarterly QA results)

2016-02-09 Thread GPC Informatics 
#327: Gather 2015 4th quarterly QA results (and 3rd quarter if feasible)
-+-
 Reporter:  mish |   Owner:  mish
 Type:  problem  |  Status:  assigned
 Priority:  major|   Milestone:  data-quality-q3
Component:  data-|  Resolution:
  quality|  Blocked By:  290, 309, 326, 351, 366, 392, 439,
 Keywords:   |  450
 Blocking:   |
-+-

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gpc-informatics 
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making the quarterly QA SQL code a little easier to find

2016-02-09 Thread Dan Connolly 
I added a link from 
DataQuality 
to gpc-qa-quarterly.

--
Dan

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