Re: SNOW Shrine Hub

[Thomas Mish]

I'm forwarding this on to Bill Taylor. It looks as if he still hasn't been 
added to the GPC-DEV list yet.


-TM

___

Thomas F. Mish Jr.  -   Informatics Systems Specialist

SMPH-ITBiomedical Informatics Services

School of Medicine and Public Health, UW-Madison

m...@wisc.edu  -  (608)616-0362


From: Gpc-dev  on behalf of Andrew 
Hangsleben 
Sent: Monday, October 9, 2017 3:41:17 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
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FW: UW Madison's r004 approved

[Thomas Mish]

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: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

[Thomas Mish]

I don't think so. 

-TM

-Original Message-
From: GPC Informatics [mailto:d...@madmode.com] 
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; mprit...@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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RE: gpc-dev 24 Jan agenda and meeting notes

[Thomas Mish]

Wisconsin (Tom) can scribe…

-TM

From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, January 23, 2017 12:50 PM
To:  ; Thomas Mish 
; rfotherg...@cmh.edu
Subject: gpc-dev 24 Jan agenda and meeting notes

I need a scribe. Next up on the list is WISC. OK, Tom or somebody? Or else CMH?

Everybody, what else for tomorrow?

  *   gpc-dev 24 Jan shared 
notes<https://docs.google.com/document/d/1ktVpm4IEPpcUi-yI--GUYYn8gTd8YEnZn8IQ9lpX9U4/edit>
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: WISC? CMH?

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

  .#275 (how much signal do we want 
back from Mytrus ADAPTABLE portal to sites to ...) 
closed<https://informatics.gpcnetwork.org/trac/Project/ticket/275#comment:3>

  i.#569 (Discussion of coded 
indexing of tissue biobanks) 
created<https://informatics.gpcnetwork.org/trac/Project/ticket/569>

ii.#28 (map Diagnoses to SNOMED CT 
in Fairview (UMN) EMR) closed 
wontfix<https://informatics.gpcnetwork.org/trac/Project/ticket/28#comment:4>

   iii.#256 (Investigate capturing 
e-consent via e-signature) closed 
wontfix<https://informatics.gpcnetwork.org/trac/Project/ticket/256#comment:8>

d.Next Meetings:

  .31 Jan

1.Scribe? CMH?
Note LRU 
schedule<https://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:92>

2.#458 MyChart for Adaptable - confirm presentation date?

3.#335<https://informatics.gpcnetwork.org/trac/Project/ticket/335> 
BuilderSaga<https://informatics.gpcnetwork.org/trac/Project/wiki/BuilderSaga> - 
Bill and Chris from U.C. Davis to join

  i.21 Feb - 
#431<https://informatics.gpcnetwork.org/trac/Project/ticket/431> text notes - 
Jay Urbain of MSOE to join

2.
Milestone:grouse-research-1<https://informatics.gpcnetwork.org/trac/Project/milestone/grouse-research-1>
 due 30 Jan
Technical questions?

3.
Milestone:snow-shrine-1<https://informatics.gpcnetwork.org/trac/Project/milestone/snow-shrine-1>
 checkpoint 30 Jan

. Quick screen-share show-and-tell next week? Week after?
No requirement for real data nor real ontologies. Even demo of current error 
messages is welcome. Points awarded for any communication between spoke and hub.

  .
#460<https://informatics.gpcnetwork.org/trac/Project/ticket/460> SNOW SHRINE 
node at UTSW<https://informatics.gpcnetwork.org/trac/Project/ticket/460>

  i.
#531<https://informatics.gpcnetwork.org/trac/Project/ticket/531> SNOW SHRINE 
node at MCRF with SCILHS PCORnet 
ontology<https://informatics.gpcnetwork.org/trac/Project/ticket/531>

4.
Milestone:next-d<https://informatics.gpcnetwork.org/trac/Project/milestone/next-d>

. #571 (characterization of data from next-d GPC sites) created by 
afurmanchuk<https://informatics.gpcnetwork.org/trac/Project/ticket/571>: “I 
would like to look at EDC reports from other GPC sites participating in next-d”.
Comment:1 from Dan: “Perhaps we should use ​GPC 
REDCap<https://redcap.gpcnetwork.org/> to collect them.”

5.
Milestone:cohort-char1<https://informatics.gpcnetwork.org/trac/Project/milestone/cohort-char1>
 (obesity) due Feb 17
#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>

. FYI: Laura, Dean setting up Weight/Health Survey Data 
Federation<https://redcap.gpcnetwork.org/redcap_v6.11.5/index.php?pid=29> GPC 
REDCap project 29

a.Reminder: slides from 
HackathonFour<https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonFour>:
 Socioeconomic Variables for Obesity 
Survey<https://docs.google.com/presentation/d/1_5vP

Fwd: RE: geocoding: how to join at tract, census block resolution?

[Thomas Mish]

Get Outlook for Android<https://aka.ms/ghei36>


From: Baker-McAlister Geoffrey I 
Sent: Monday, January 9, 2017 2:49:35 PM
To: Thomas Mish
Subject: RE: geocoding: how to join at tract, census block resolution?

Hey Tom,
So, this is what I was relaying to you and Debbie last Friday. There are 5 
levels in the US Census hierarchy:


1.   State (two digit - 55 for WI)

2.   County (three digit - 045 for Dane)

3.   Tract (6 digit - I don't have a good example, but you get the idea)

4.   Block Group (1 digit)

5.   Block (I think 2 digit, honestly, I don't know for sure. I hardly ever 
work with blocks)

When someone says, "give me the block group of 301 S. Westfield Rd, Madison WI, 
53717," what they are really asking for is the concatenation of 1, 2, 3 and 4. 
If you are only given 4, it will not tell you anything.

Geoff

From: Thomas Mish [mailto:m...@wisc.edu]
Sent: Monday, January 09, 2017 2:42 PM
To: Baker-McAlister Geoffrey I
Subject: Fwd: geocoding: how to join at tract, census block resolution?


Geoff

Is there any guidance or words of wisdom you could offer to other groups 
looking at this problem.

TM

Get Outlook for Android<https://aka.ms/ghei36>


From: Gpc-dev 
mailto:gpc-dev-boun...@listserv.kumc.edu>> 
on behalf of Dan Connolly mailto:dconno...@kumc.edu>>
Sent: Monday, January 9, 2017 2:38:02 PM
To: vanri...@umn.edu<mailto:vanri...@umn.edu>
Cc: mailto:gpc-dev@listserv.kumc.edu>>
Subject: geocoding: how to join at tract, census block resolution?

Hi Dave,

More questions!

I'm copying gpc-dev so we can all learn together. Before you reply all, note 
the public archive http://listserv.kumc.edu/pipermail/gpc-dev/

I'm working with Maren and Sravani on this stuff. Joining on zip code was 
straightforward: we used the zcta5 column of 
acs_20135a/zcta_860/ge.00_file.dat.gz.

But now we're trying to join on tract and census block. What columns of 
acs_20135a/blck_grp_150/ge.00_file.dat.gz and 
acs_20135a/tract_140/ge.00_file.dat.gz should we use? What are their primary 
key columns? Which documentation would  tell us this?

BLKGRP looks like a single-digit number; it's clearly not a unique key to the 
blck_grp_150 data.

TRACT is a bigger number, but it's not a unique key to tract_140 either. It 
seems to be unique within state, though. Is that right? Should we join TRACT_ID 
and ST_ABRV from geocoded_kumc.txt with TRACT and STUSAB of tract_140?

Have any other GPC sites figured this out yet? MU? UTHSCSA?

For reference, these are the columns of our kumc_geocoded.txt data:

'OID,Join_Count,TARGET_FID,Loc_name,Status,Score,Match_type,'
'X,Y,Match_addr,DISP_LON,DISP_LAT,SIDE,'
'ARC_Address,ARC_City,ARC_State,'
'ARC_Zip,ADDRESS,CITY,STATE,ZIP,New_X,New_Y,ID,BLOCK_ID,'
'FIPSST,FIPSCO,FIPSSTCO,TRACT_ID,ST_ABRV,CO_NAME,ST_NAME

context:
https://informatics.gpcnetwork.org/trac/Project/ticket/140
https://informatics.gpcnetwork.org/trac/Project/ticket/350

--
Dan
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Re: Height+Weight survey -- instructions for sending the result?

[Thomas Mish]

In case nobody has answered yet, instructions can be found here: 
https://informatics.gpcnetwork.org/trac/Project/ticket/379


Comments 5 & 6 are the most relevant.


-TM



___

Thomas F. Mish Jr.  -   Informatics Systems Specialist

SMPH-ITBiomedical Informatics Services

School of Medicine and Public Health, UW-Madison

m...@wisc.edu  -  (608)616-0362


From: gpc-dev-boun...@listserv.kumc.edu  on 
behalf of Pedersen, Jay G 
Sent: Tuesday, April 19, 2016 5:36:18 PM
To: gpc-dev@listserv.kumc.edu
Subject: Height+Weight survey -- instructions for sending the result?

Hi,

Can anyone indicate the method for sending the resulting R Data Builder file 
for the Height and Weight survey?  My understanding is that it goes to San 
Antonio.  I did not see detailed instructions on sending the result.  The 
result file is somewhat large -- a 4GB file (SQLITE ".db" file).

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)

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, 
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RE: Recruiting via MyChart for PCORI Study Participation

[Thomas Mish]

Brian,

You and a couple of other folks have asked about an off-campus or reprise of 
the presentation. We were going to reprise the Recruiting for MyChart for PCORI 
Study Participation presentation for our internal UWHealth - Health Information 
Management Center (HIMC) at their staff meeting on May 3rd.  I talked with the 
director of that group and he graciously extended a welcome to anyone from the 
GPC who'd like to join in. The HIMC staff consists mostly of data analysts, 
project managers, ETL engineers, and other data geeks and would fit in well 
with the GPC-DEV and GPC-PM groups.

That presentation is going to be May 3rd from 8:30am - 9:30am. We'll have a 
WebEx (Cisco's remote meeting solution) setup for that meeting and regularly 
have a number of remote participants. I can provide details to whomever is 
interested in joining us that morning.

-TM


From: Gryzlak, Brian M [mailto:brian-gryz...@uiowa.edu]
Sent: Wednesday, March 16, 2016 9:36 AM
To: Thomas Mish
Subject: RE: Recruiting via MyChart for PCORI Study Participation

Tom is there a way for off-campus folks to listen in?
-Brian
From: 
gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu> 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Thomas Mish
Sent: Wednesday, March 16, 2016 8:37 AM
To: 'gpc-dev@listserv.kumc.edu' 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: FW: Recruiting via MyChart for PCORI Study Participation

For those wondering, the UW-Madison presentation on our combined MyChart/REDCap 
study for the Greater Plains Collaborative is RAC08 in the Research Advisory 
Council tract. It will occur at 2:30pm on Tuesday April 12th of the Epic Expert 
Group Meetings (XGM). For others attending XGM, is there any interest in a GPC 
gathering on Tuesday evening?
RAC08
Recruiting via MyChart for PCORI Study Participation
2:30 PM 3:15 PM
Clinical Data Research Networks are PCORI funded projects, aimed at using EHR 
systems as tools for clinical research. As a member of the Greater Plains 
Collaborative CDRN, the UW-Madison team was asked to reach out to UW Health 
patients matching the eligibility criteria for the Weight & Health study. A 
combined MyChart/REDCap solution was developed. Patient response to this 
outreach was extremely positive. The presentation describes the experience of 
developing and implementing the solution, as well as a detailed presentation of 
the results. Learning Objectives: Describe and discuss the process of planning, 
developing, and implementing recruitment technologies using MyChart and REDCap. 
Discuss the results of a questionnaire filled by patients, regarding their 
opinions about the use of electronic means to engage in clinical research. 
Discuss ethical and privacy issues around the MyChart/REDCap solution being 
presented.
Years live on functionality: More than 5. This session also relates to: MyAC, 
PHF. Research, Patient Engagement, Recruitment. UW Health (WI) Audience: All 
Focus: Enterprise
-TM

PS: Thanks again to the multitude of people at UWHealth, SMPH and across the 
GPC that went into making this possible.
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SMPH-ITBiomedical Informatics Services
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m...@wisc.edu<mailto:m...@wisc.edu>  -  (608)265-9228 or (608)616-0362

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FW: Recruiting via MyChart for PCORI Study Participation

[Thomas Mish]

For those wondering, the UW-Madison presentation on our combined MyChart/REDCap 
study for the Greater Plains Collaborative is RAC08 in the Research Advisory 
Council tract. It will occur at 2:30pm on Tuesday April 12th of the Epic Expert 
Group Meetings (XGM). For others attending XGM, is there any interest in a GPC 
gathering on Tuesday evening?
RAC08
Recruiting via MyChart for PCORI Study Participation
2:30 PM 3:15 PM
Clinical Data Research Networks are PCORI funded projects, aimed at using EHR 
systems as tools for clinical research. As a member of the Greater Plains 
Collaborative CDRN, the UW-Madison team was asked to reach out to UW Health 
patients matching the eligibility criteria for the Weight & Health study. A 
combined MyChart/REDCap solution was developed. Patient response to this 
outreach was extremely positive. The presentation describes the experience of 
developing and implementing the solution, as well as a detailed presentation of 
the results. Learning Objectives: Describe and discuss the process of planning, 
developing, and implementing recruitment technologies using MyChart and REDCap. 
Discuss the results of a questionnaire filled by patients, regarding their 
opinions about the use of electronic means to engage in clinical research. 
Discuss ethical and privacy issues around the MyChart/REDCap solution being 
presented.
Years live on functionality: More than 5. This session also relates to: MyAC, 
PHF. Research, Patient Engagement, Recruitment. UW Health (WI) Audience: All 
Focus: Enterprise
-TM

PS: Thanks again to the multitude of people at UWHealth, SMPH and across the 
GPC that went into making this possible.
___
Thomas F. Mish Jr.  -   Informatics Systems Specialist
SMPH-ITBiomedical Informatics Services
School of Medicine and Public Health, UW-Madison
m...@wisc.edu  -  (608)265-9228 or (608)616-0362

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2015 Q4 Quality Results

[Thomas Mish]

2015 Q4 Quality Results
This quarter we added data to get at the quality of our alignment with the GPC 
standard ontology mapping and our ability to show results in two key areas, the 
data used for the breast cancer cohort within the NAACCR registry and the data 
we had predicted would be useful as a part of the height and health cohort. In 
the scripts, there were two categories of results that were available for any 
given value.

* Either the specific value was going to be found within the GPC 
standard ontology:

o   And the value was found within the exact matching GPC ontology

o   And the value was not found within the matching GPC ontology

* Or the site overrode the default standard ontology and specified a 
different location for the value:

o   And the value was found at a site specified non-matching ontology spot

o   but the value was not found at the site specified non-matching ontology 
spot.

Given the data pre-processing R scripts that Kansas wrote helped to point out 
ontology matching errors we would expect good matching in terms of ontology 
alignment within the NAACCR data, and in fact we did. The term matching rate 
was over 99% among the subset of fields measured and sites responding to the 
quality query. Just because the terms match, however, doesn't mean that the 
data was found there, and only 50% of the results were actually found in the 
expected spots.

For the measures selected as being generally useful for the height and health 
cohort, things were much different. The ontology matching within the databases 
dropped to 35%. However, the individual sites were better and understanding 
their data and results were found almost 72% of the time at the reporting sites.

Note: One of the latest upgrades to the GPC REDCap site made the existing data 
dictionary incompatible (a hard limit on variable name lengths) and it can no 
longer be exported and reimported without some work. This will mean some 
additional changes will have to be accommodated in the next quality run.
___
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SMPH-ITBiomedical Informatics Services
School of Medicine and Public Health, UW-Madison
m...@wisc.edu  -  (608)616-0362

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RE: [gpc-informatics] #379: Link EHR data to Health and Medical Research Family Survey (HMRFS) 2 results

[Thomas Mish]

See response below...

-Original Message-
From: Alex Bokov [mailto:bo...@uthscsa.edu] 
Sent: Thursday, March 03, 2016 12:01 PM
To: gpc-dev@listserv.kumc.edu; gkowal...@mcw.edu; dconno...@kumc.edu; 
b...@uthscsa.edu; rwait...@kumc.edu; rfotherg...@cmh.edu
Cc: Thomas Mish ; kwa...@uwhealth.org; bzscho...@kumc.edu
Subject: Re: [gpc-informatics] #379: Link EHR data to Health and Medical 
Research Family Survey (HMRFS) 2 results



On 03/03/2016 09:01 AM, GPC Informatics wrote:
>   OK, so Jay / UNMC no longer has the ball...
He only no longer has the ball for as long as it takes me to read the emails, 
and it's highly likely that he will then again have the ball.
>   Alex, a common pattern with all-sites tickets like this one is: once we're
>   "almost there," close this one and make separate tickets for the remaining
>   sites. In this case, we didn't separate "collect the data" from "link it"
>   so we shouldn't close this one until some level of linking is done.
>
>   Meanwhile, I escalated the UTSW situation to its own ticket: #487. For MCW
>   and WISC, I'm OK to continue to track them here. And I'll pick on George /
>   MCW for the assignment, since you named them first, Alex.



Also, even though WISC is working on deploying DataBuilder, they should already 
be able to upload the survey data and survey data dictionary from their local 
REDCap. Tom, would it be be possible for you guys to do that?

-Yes that should be possible. I have to get the transfer of data OK'd, but that 
shouldn't be an issue with this data.

-TM

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RE: Gather 2015 4th quarterly QA results

[Thomas Mish]

Dan and I had a *very* brief conversation at the last Hackathon about the 
possibility of performing some of the queries against Babel centrally instead 
of asking each site to run code. This would be another way to simplify the 
quality query process.

I would assert that the goal besides getting a meaningful handle on the quality 
of the data across the sites is also to make quality a byproduct of the natural 
i2b2 process and not something that should put an undue burden on the 
individual sites on a quarterly basis. Running queries centrally against Babel 
would be a way another way to achieve this.

-TM



From: Green, Timothy A. [mailto:green...@health.missouri.edu]
Sent: Monday, February 15, 2016 3:21 PM
To: Dan Connolly; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

Thanks for sharing these. I am interested in an implementation agnostic QA 
process.  These scripts and the qa val list make a decent starting point to 
build some dynamic i2b2 queries that leverage the metadata layer.  As probably 
the only site with a vested interest in altering how the QA scripts work, I 
think it's fair for MU to take the lead on looking into it.

In the interim, we are going to focus on finishing our NAACCR load and then do 
something quick and dirty for the 2015/Q4 and 2016/Q1 QA results.


From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 3:10 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

Silly me... didn't give a URL in the first place:

regression test driver:
https://informatics.kumc.edu/work/browser/heron_load/test_heron_query.py

performance test driver:
https://informatics.kumc.edu/work/browser/heron_load/query_performance.py

The queries are captured this way:
https://informatics.kumc.edu/work/browser/heron_load/capture_query.py

The code is kinda... well... I'm not sure I'd write it that way today.

The gist of it is: we use capture_query.py to grab matching rows from 
qt_query_master and save (among other things) the I2B2_REQUEST_XML; then we 
make HTTP requests just like the web client would to log-in and replay the 
request.

--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 3:03 PM
To: Dan Connolly; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results
Indeed, I'm all for the forward looking approach.  What driver are you using 
for batch mode i2b2 queries?

From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 3:00 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

My first thought was: what does this have to do with the patient_dimension? It 
seems to only care what paths you use at your site.

But I think my tiny brain has finally absorbed the issue...

Even though our demographics ontology design is based on query paths, those 
query paths normally get looked up in the metadata table, which may say to look 
the path up in the concept_dimension, but may also say: we're done with the 
path; go look in some column of another dimension table.

This makes me wish we used more i2b2 queries for our QA stuff. I suppose we're 
headed that way with SHRINE/SNOW... Meanwhile, I wonder how many sites have the 
capacity to run a suite of i2b2 queries in lights-out fashon. We do this in the 
form performance and regression testing for HERON, but we should be able to 
straightforwardly adapt it for QA work.

That is to say: "some hard coded queries against patient_dimension" is one 
reasonable approach, but perhaps a more forward-looking approach would be some 
work-alike i2b2 queries.

--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 2:43 PM
To: Dan Connolly; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results
Yes, onboard with the readme, that is the other work we have to do, which is 
finding our paths that match the concept under QA.

Here is the same concept from the shared code, slightly different syntax.  I 
sent you a version we had already converted to mssql ourselves last December, 
before the code below was shared.  This can be found on line 95 here 
(https://bitbucket.org/gpcnetwork/gpc-qa-quarterly/src/e6d33c16e8691529f37025c36163bd3377d7e9e8/qa_mssql.sql?at=default&fileviewer=file-view-default).

select
v.VARIABLE_NAME
,count(distinct o.PATIENT_NUM) as RESULT
FROM $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_VAL_LIST] v
JOIN $(DataDB).[dbo].[CONCEPT_DIMENSION] c on (c.CONCEPT_PATH like 

RE: Gather 2015 4th quarterly QA results

[Thomas Mish]

I think that very early on in the GPC conversations we covered a lot of ground 
in the fact vs patient dimension conversation. I know that here at Madison we 
altered the way we organized our i2b2 data at the time to that we were more 
like the rest of the GPC. I understand the angst over changing. I'd love to see 
what you doing/have done to make the script more neutral on this issues. We'll 
incorporate them as best as possible for next time to minimize the churn.

-TM

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, February 15, 2016 11:50 AM
To: Green, Timothy A. ; Mosa, Abu S. 

Cc: McNeeley, Todd A. ; 
 
Subject: RE: Gather 2015 4th quarterly QA results

To the extent that I did any of the writing of the QA scripts, I made no 
assumption about fact table vs. patient dimension. All our ontology design 
decisions regard paths. I haven't looked at all the code in detail, though. If 
there is such an assumption, it should be straightforward to refer us to one or 
more lines or statements that exhibit the assumption. Would you please give 
such details? Or just run the script and give us one or more diagnostic 
messages that show the assumption in action?

And as to "the relatively simple task of mapping..." that's the point of the QA 
scripts: to measure progress on that mapping. If you run the scripts and get 
some zeros, the script is still working correctly. It correctly shows that 
you're not finished. (You're not alone. KUMC has plenty of work to do in this 
area, for example.)

--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 10:38 AM
To: Mosa, Abu S.; Dan Connolly
Cc: mailto:gpc-dev@listserv.kumc.edu>>; McNeeley, 
Todd A.
Subject: RE: Gather 2015 4th quarterly QA results
The patient demographics are stored in our i2b2 in the person dimension.  The 
QA scripts are written with the assumption that all data is stored in the fact 
table.  There is no provision for the script to leverage the ontology 
architecture to determine the storage location of the various pieces of data.  
I'm sure it was done that way to simplify the script, but it does ignore a 
pretty major feature of i2b2: the ontology mapping functionality.  This makes 
it less portable to sites that have a different implementation of the ontology. 
 I don't characterize a difference in implementation a problem in the data 
warehouse.

Keep in mind that MU had an i2b2 instance back in 2014, and the MU architecture 
was established before joining the GPC.  It would be work to either shift our 
demographics storage (and additional storage capacity), or to rewrite the QA 
scripts.  We will opt to rewrite the QA scripts, but to do it in a portable way 
(i.e. we could share our changes back to the GPC) will require some complexity 
of coding to leverage the ontology framework in i2b2.  We may have to opt for 
hardcoding our version against the dimension table.

Aside from that, we still have the relatively simple task of mapping our 
concept codes/paths to get the remainder (non-demographic part) of the script 
to work correctly.

Tim



From: Mosa, Abu S.
Sent: Monday, February 15, 2016 10:20 AM
To: Dan Connolly
Cc: mailto:gpc-dev@listserv.kumc.edu>>; Green, 
Timothy A.; McNeeley, Todd A.
Subject: RE: Gather 2015 4th quarterly QA results

I would defer this to Tim and Todd to share their thoughts on this. Thanks. 
--Mosa

From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 10:03 AM
To: Mosa, Abu S. mailto:mo...@health.missouri.edu>>
Cc: mailto:gpc-dev@listserv.kumc.edu>> 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

What are the symptoms when you try to run the QA scripts, Mosa? What 
diagnostics do you get?

The premise of the QA scripts is that if they don't run, that's a problem with 
your data warehouse. Perhaps there are actually problems with the scripts, but 
if so, we need details on what those problems are. Also, we have a shared 
source code repository in 
gpc-qa-quarterly. So if you 
make changes, please strive to make them portable to other sites.

p.s. I presume it's OK to share this thread with gpc-dev, as it regards group 
technical work.

--
Dan

From: Mosa, Abu S. [mo...@health.missouri.edu]
Sent: Friday, February 12, 2016 4:41 PM
To: Dan Connolly
Subject: Gather 2015 4th quarterly QA results
Hi Dan,

I talked with our technical team about generating the 2015 4th quarterly 
report. They looked into the MSSQL code that you referred to me on BitBucket. 
They advised that major re-writing effort is needed in order to localize the 
scripts to be able to run on our i2b2 data model. They are currently focusing 
on the Phase I implementation (specifically tumor registry data load) which 
they target to complete by end of this month. So

2016-01-19 GPC-DEV minutes...

[Thomas Mish]

All, please fine the gpc-dev meeting minutes attached in PDF form.

-TM




GPCDevMeetingNotes19January2016.pdf
Description: GPCDevMeetingNotes19January2016.pdf
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RE: Agenda for today's call?

[Thomas Mish]

Sounds good...

-TM

From: Nathan Graham [mailto:ngra...@kumc.edu]
Sent: Tuesday, January 19, 2016 10:48 AM
To: Thomas Mish; 'gpc-dev@listserv.kumc.edu'
Subject: RE: Agenda for today's call?

Tom,

Last I heard (just a few moments ago) is that Dan is out sick today.  As far as 
I'm concerned, I'd say yes let's start with a copy of the notes from last week. 
 We can at least review todo items from last week.

From: 
gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu> 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Thomas Mish
Sent: Tuesday, January 19, 2016 10:45 AM
To: 'gpc-dev@listserv.kumc.edu'
Subject: Agenda for today's call?

Dan,

Keith and I both looked and neither of us has seen an agenda for the call for 
today? Should I just start one from scratch 
(https://docs.google.com/document/d/14ovzyGZTrb4vC5JJPuRmfemUg7uTgiEodlLnC7lYemw/edit?usp=sharing)?

-TM

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Agenda for today's call?

[Thomas Mish]

Dan,

Keith and I both looked and neither of us has seen an agenda for the call for 
today? Should I just start one from scratch 
(https://docs.google.com/document/d/14ovzyGZTrb4vC5JJPuRmfemUg7uTgiEodlLnC7lYemw/edit?usp=sharing)?

-TM

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FW: How's It Going

[Thomas Mish]

For anyone wanting to take a look at the US census data, our old friend Nathan 
Wilson has this to offer.

-TM

From: Nathan Wilson [mailto:wilsn...@yahoo.com]
Sent: Wednesday, January 06, 2016 7:49 AM
To: Thomas Mish
Subject: How's It Going

Hi Tom,

Hope everything is going well in Wisconsin.

I was at a conference the other day and learned something that you might be 
interested in.  Apparently Census has released CitySDK which is a DEV Kit built 
around the Census data.

Nathan

CitySDK - US Census Bureau<https://uscensusbureau.github.io/citysdk/>




[image]<https://uscensusbureau.github.io/citysdk/>











CitySDK - US Census Bureau<https://uscensusbureau.github.io/citysdk/>
The US CitySDK has been created by the US Census Bureau in close collaboration 
with contributors in both the public and private sector.


View on uscensusbureau.github.io<https://uscensusbureau.github.io/citysdk/>

Preview by Yahoo






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How long do other sites leave the Height/Health REDCap survey active?

[Thomas Mish]

All,

I don't recall this conversation and or language talking about this issue, but 
I was curious how long each of our sites have left the H/W REDCap survey active 
after sending out the invitation. We didn't send our out until recently 
(mid-December) and are still getting a handful (2-10) every day yet. Plotting 
response rates seems to leave me in doubt that this will ever tail off 
completely but I'm assuming that eventually we'll reach a point of diminishing 
returns. Do other sites still have their REDCap surveys active? If not, at what 
point did you deactivate the survey?

-TM
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RE: Q1 2016 QA, GPC redcap access (was: #290)

[Thomas Mish]

Checking to see, access for "s156...@utsouthwestern.edu (Susan Morrison)" had 
not been added to the "GPC Quarterly QA Check Repository" project yet. It has 
now.

-TM

-Original Message-
From: Dan Connolly [mailto:dconno...@kumc.edu] 
Sent: Monday, January 04, 2016 11:44 AM
To: gpc-dev@listserv.kumc.edu; Thomas Mish ; Nathan Graham 
; Brittany Zschoche ; 
srdmorri...@gmail.com
Cc: campb...@unmc.edu
Subject: RE: Q1 2016 QA, GPC redcap access (was: #290)

I don't think we've started on Q1 2016 QA stuff.

If you're having trouble accessing https://redcap.gpcnetwork.org/ , note where 
it says "If you require assistance or have any questions about REDCap, please 
contact Medical Informatics Support at KUMC. ". i.e. misupp...@kumc.edu

--
Dan


From: GPC Informatics [d...@madmode.com]
Sent: Tuesday, December 15, 2015 6:27 PM
To: m...@wisc.edu; Dan Connolly; Nathan Graham; Brittany Zschoche; 
srdmorri...@gmail.com
Cc: campb...@unmc.edu
Subject: Re: [gpc-informatics] #290: integrate interim report enrollment data 
collection with quarterly QA review

#290: integrate interim report enrollment data collection with quarterly QA 
review
-+--
 Reporter:  preeder  |   Owner:  mish
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-quality-q3
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  327, 408 |
-+--

Comment (by susandm):

 Are the first quarterly's due now or  are we in waiting status?  I can's  
access my gpc redcap and so far this has been ok but would need to see if  this 
is permissions or not.

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/290#comment:9>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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RE: Tickets 439 441

[Thomas Mish]

Jim,

I was chatting with Brad from MCW gloating about the Packers victory. Brad 
noticed something odd with the UNMC numbers that I entered in for you guys. I'm 
not sure what happened, but your Male/Female numbers are drastically different 
than what they've been in the past. It is my belief that I entered what you 
sent to me, but they don't seem to be in line with the other sites, not what 
UNMC had delivered for #'s previously. Where these filtered by "active patient"?

-TM

From: Campbell, James R [mailto:campb...@unmc.edu]
Sent: Monday, December 14, 2015 6:30 AM
To: Thomas Mish 
Cc: gpc-dev@listserv.kumc.edu; Buzalko, Russell J ; 
McClay, James C 
Subject: Tickets 439 441


Tom

I realize that I d0onot recall where to submit this table?  We have some 
discrepancy in totals for the for the spreadsheet, but I understood this was 
NLT Monday

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.
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RE: Tickets 439 441

[Thomas Mish]

The URL was: 
https://redcap.gpcnetwork.org/redcap_v6.2.2/ProjectSetup/index.php?pid=19

I'll upload your results for you.

-TM

From: Campbell, James R [mailto:campb...@unmc.edu]
Sent: Monday, December 14, 2015 6:30 AM
To: Thomas Mish 
Cc: gpc-dev@listserv.kumc.edu; Buzalko, Russell J ; 
McClay, James C 
Subject: Tickets 439 441


Tom

I realize that I d0onot recall where to submit this table?  We have some 
discrepancy in totals for the for the spreadsheet, but I understood this was 
NLT Monday

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.
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FW: Agenda for GPC-DEV call tomorrow

[Thomas Mish]

Dan/Brittany,

There were some questions on the phone call regarding the estimated 
time-to-deliver on the CDM 3 data. Seeing as we are dependent on Harvard 
finished/finalizing the code, we are all stuck behind them as a final 
dependencies. We agreed on the phone call to assume that their code would be 
delivered with Q1 2016. That base assumption would drive all the rest of our 
estimates at each of the sites.

There was also some concern about the 12/2 delivery date. At least one of the 
sites was hoping that they could deliver this estimate by the end of the week. 
Is there something magical driving the 12/2 deadline that we need to have the 
data in by?

-TM

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Thomas Mish
Sent: Monday, November 30, 2015 2:52 PM
To: gpc-dev@listserv.kumc.edu
Subject: Agenda for GPC-DEV call tomorrow

Thankt's to Brittany's help, here's a link to tomorrow's GPC-DEV call:
https://docs.google.com/document/d/1XZPV0qeq52I5uv5GaWPTdTN9ZI8bxOuh_CjRc_rVAWk/edit

An ahead of time thanks to Hillary for setting up the phone call for tomorrow 
morning and to Nathan Graham for agreeing to take the minutes.

-TM
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SMPH-ITBiomedical Informatics Services
School of Medicine and Public Health, UW-Madison
m...@wisc.edu<mailto:m...@wisc.edu>  -  (608)616-0362

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Agenda for GPC-DEV call tomorrow

[Thomas Mish]

Thankt's to Brittany's help, here's a link to tomorrow's GPC-DEV call:
https://docs.google.com/document/d/1XZPV0qeq52I5uv5GaWPTdTN9ZI8bxOuh_CjRc_rVAWk/edit

An ahead of time thanks to Hillary for setting up the phone call for tomorrow 
morning and to Nathan Graham for agreeing to take the minutes.

-TM
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School of Medicine and Public Health, UW-Madison
m...@wisc.edu  -  (608)616-0362

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RE: gpc-dev 17 Nov agenda and meeting notes

[Thomas Mish]

Do we have a draft agenda set for Hackathon 3 yet? So far I’ve seen

· a desire to discuss patient reported outcomes.

o   There’s representing them in i2b2

o   As well as conversations about plumbing and how to get at them in the first 
places.

· Sessions for helping the new sites get up and running

Have there been other suggestions in the REDCap survey that have come back?

-TM

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, November 16, 2015 1:43 PM
To:  
Subject: gpc-dev 17 Nov agenda and meeting notes

What else for tomorrow?

17 Nov gpc-dev meeting 
notes

current proposal:




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

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

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

  i.today's scribe: TBD

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

*

d.Next Meeting: 24 November Scribe Volunteer?

2.Milestone: 
cohort-char1

.  #404 FYI: 
stay tuned for instructions on sharing de-id survey results

3.Milestone:bc-agg-1

.  #385 Collect BC 'Patient Mapping File' from from breast cancer survey 
sites

4.Milestone: 
data-quality-q3

.  #196 (Should the "active patient" be based on visits or encounters?) 
closed 
invalid - as-designed

a.refined scope for #327 
 Gather 2015 3rd, 
4th quarterly QA results

   .
#290 integrate 
interim report enrollment data collection with quarterly QA review

  i.
#326 Quality checks 
for terminology alignment (with fact volume) for GPC ontologies

ii.
#351 Race, 
ethnicity data quality checks don't match babel counts

5.Milestone: 
data-domains3

.  #78 (shared GPC RxNORM/NDFRT medications ontology) 
closed

a.#67 (Demographics ontology and value sets, e.g. age) 
closed

b.#158 (usable view of LOINC lab terms) 
closed

c.milestone target clarified: reproducible GPC, CDM refresh 
(#160)

6.Milestone: 
drn-query-1

.  Notes from 11 Nov meeting with DSSNI?

a.what’s left on 
#240?

7.Milestone: 
cohort-char-als

.  #380: follow-up from Nov 12 
meeting

8.Milestone: 
bariatric-study-data

.#283: determine GPC funding status forbariatric 
study   McClay, 
James C

9.HERON etl-dev

.  #410 (unit conversion in HERON flowsheet ETL) opended, 
closed



--
Dan
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RE: OK to share babel ontologies with selected collaborators from NYC-CDRN, SCILHS CDRNs?

[Thomas Mish]

No objections from WISC.

-TM

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Wednesday, November 04, 2015 3:46 PM
To:  
Subject: OK to share babel ontologies with selected collaborators from 
NYC-CDRN, SCILHS CDRNs?

We've discussed collaboration with SCILHS at length. Folks from the NYC-CDRN 
(Cornell, in particular) are using the HERON code and working through Tumor 
Registry integration. Access to share tables via babel's web-based SQL IDE 
would facilitate the collaboration.

Our current agreement 
(#76) is "share with 
GPC, not all of PCORI nor public ". Is it OK if we extend this to selected 
collaborators from other CDRNs, at the discretion of Russ, Nathan, and myself?

--
Dan
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UMN Q3 quality results in the GPC REDCap database.

[Thomas Mish]

Justin,

I went to do an import on the dataset you sent me and ran into no errors. The 
way you have your data import set the record format is “Rows” (most of the QA 
datasets use “Columns” – but no big deal); the dates are all the default 
format, those are really the only import options. I have no clue why this 
worked for me and not for you. I’m a little surprised, I thought I’d at least 
have a bit of a tussle on my hands this morning. I guess that leaves me with a 
few extra minutes for an extra cup of coffee this morning.

Cheers and congrats on being the first group to import your results into the 
REDCap database.

[cid:image001.jpg@01D10D6A.757DD3D0]

-TM



From: dalex...@umn.edu [mailto:dalex...@umn.edu] On Behalf Of Justin Dale
Sent: Thursday, October 22, 2015 8:30 AM
To: Thomas Mish
Subject: Re:

Thanks.  UMN Q3 file attached. Let me know if you see anything that would be 
causing the errors.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu<mailto:jd...@umn.edu>

On Thu, Oct 22, 2015 at 8:25 AM, Thomas Mish 
mailto:m...@wisc.edu>> wrote:

Previous results as reported by REDCAp
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Re: final enrollment counts for UMN

[Thomas Mish]

Justin,

Can I give you a call tomorrow morning around 8am?

Thomas Mish
School of Medicine and Public Health
UW-Madison

Sent by Outlook<http://taps.io/outlookmobile> for Android



On Wed, Oct 21, 2015 at 2:28 PM -0700, "Justin Dale" 
mailto:jd...@umn.edu>> wrote:

Running into issues again when trying to import our csv into the Redcap 
project.  Basically telling me that every field has an invalid value, which is 
clearly not the case.  We ran into issues last time but that had to do with the 
word "NULL" being listed as a value and was fixed by Tom M. when he cleared 
those out.  Tried that again but still getting errors.  Any ideas or help would 
be appreciated.  We generated the csv using Nathan's SQL code (re: ticket #97).

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu<mailto:jd...@umn.edu>
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RE: #350 geocoding: distribute census, ACS data to sites

[Thomas Mish]

From: 
gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Justin Dale
Sent: Wednesday, October 07, 2015 1:44 PM
To: Dan Connolly
Cc: mailto:gpc-dev@listserv.kumc.edu>>
Subject: Re: #350 geocoding: distribute census, ACS data to sites

There is one compressed geocoded file for each site.  Sizes range from 45MB - 
175MB.  There is also a compressed block crosswalk file that is 114MB and some 
additional documentation files.

I think the easiest delivery method would be to use Google Drive. Can each site 
provide me with contact(s) and email addresses who will be responsible for 
downloading the files?  I will move the files into the appropriate folders and 
then share accordingly.


  1.  CMH -
  2.  KUMC -
  3.  MCRF- Laurel Verhagen – 
verhagen.lau...@mcrf.mfldclin.edu
  4.  MCW -
  5.  MU – Abu Mosa 
(mo...@health.missouri.edu)
  6.  UNMC -
  7.  UTHSCSA -
  8.  UTSW -
  9.  WISC – m...@wisc.edu
Thanks.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Tue, Oct 6, 2015 at 10:36 AM, Dan Connolly 
mailto:dconno...@kumc.edu>> wrote:
Thanks for the update.

If it's at all convenient, don't make Mei a single point of failure. The goal 
is to distribute the data to the sites, so if you can give a couple people at 
each site sFTP access, please do. At least give Nathan and myself access so we 
can help Mei.

I expect what we'd do is turn around and use 
redcap.gpcnetwork.org
 to distribute the files, so if you want to skip right to that, please do. We'd 
probably make a separate redcap project for each site. (a little tedious, but 
not too bad). File sizes might be an issue... we'll see.

Perhaps google drive or box is appropriate for these data...

--
Dan

From: dalex...@umn.edu 
[dalex...@umn.edu] on behalf of Justin Dale 
[jd...@umn.edu]
Sent: Monday, October 05, 2015 8:59 PM
To: Dan Connolly
Cc: mailto:gpc-dev@listserv.kumc.edu>>
Subject: Re: gpc-dev 6 Oct agenda and meeting notes
I need to send my regrets for tomorrow's call as I will be out of the office.

I've asked David for the location of the geocoding files.  Once I have that 
info I will place the files in the same sFTP directory that the original data 
was delivered and will let Mei Liu from KUMC know.

I would have put this in the comments info on the trac 
ticket
 but I just reset my password and now I can'l login.  I believed this happened 
last time I tried to reset my password.  Nathan Graham, can you assist with 
this again?  This is for my jdale username.  Thanks.



Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Mon, Oct 5, 2015 at 5:11 PM, Dan Connolly 
mailto:dconno...@kumc.edu>> wrote:
What else for tomorrow?

shared notes for Oct 
6;
 current snapshot:



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

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

b.roll: all 12 
DevTeams

gpc-dev 8/25/2015 Agenda & Meeting notes

[Thomas Mish]

Good afternoon all,

Here's the 
agenda
 for the meeting tomorrow. George from MCW has graciously volunteered to step 
in to take minutes and you're all stuck with me chairing the meeting. See you 
all tomorrow at 11am.

-TM
___
Thomas F. Mish Jr.  -   Informatics Systems Specialist
SMPH-ITBiomedical Informatics Services
School of Medicine and Public Health, UW-Madison
m...@wisc.edu  -  (608)616-0362


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RE: PCORnet Initial Basic Query incomplete for 5 sites - Dev call agenda item?

[Thomas Mish]

I had been told our PopMedNet install was complete. It appears that we've 
missed a confirmation step. Keith, the guy working on it is out until next 
week. I'm assuming we just need to take the last step which should happen the 
week he returns. Hence, I anticipate closing the loop by the 21st at WISC.

-TM

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, August 10, 2015 9:49 AM
To: Verhagen, Laurel A ; 
gpc-dev@listserv.kumc.edu
Subject: RE: PCORnet Initial Basic Query incomplete for 5 sites - Dev call 
agenda item?

Bhargav is out today. The person who was our PMN administrator, Brandon, has 
moved on from KUMC. And his replacement in this role, Mike, is out for a while 
having become the father of twins a few days ago.

But there's never any excuse not to give an estimate; anybody can throw a dart 
at the calendar and then give more info as it becomes available... so...

At present course and speed, it'll be some 3 months before we complete the 
initial basic query.

Here's hoping we manage to get it done sooner.

--
Dan


From: Dan Connolly
Sent: Friday, August 07, 2015 4:10 PM
To: Verhagen, Laurel A; 
gpc-dev@listserv.kumc.edu
Subject: RE: PCORnet Initial Basic Query incomplete for 5 sites - Dev call 
agenda item?
I guess this answers my question about what's left to do on 
#154. Bhargav, ETA?

Tom, Keith, ETA for WISC? 
#166

MCW... Brad? George?

CMH... Nate? #161

UTSW... Susan? Phillip?

I wonder why we don't have open tickets on MCW and UTSW. And I suppose there's 
a list of the popmednet administrators at each site somewhere, but I don't have 
it handy just now.

If necessary, we can talk about this by phone. But it seems straightforward to 
collect ETA info by email.

--
Dan

From: Verhagen, Laurel A [verhagen.lau...@mcrf.mfldclin.edu]
Sent: Friday, August 07, 2015 3:25 PM
To: gpc-dev@listserv.kumc.edu; Dan Connolly
Subject: PCORnet Initial Basic Query incomplete for 5 sites - Dev call agenda 
item?
Dan,

Can we add this as a topic for the Dev call next week?

Thanks,
Laurel

From: Petro, Lindsey [mailto:lindsey_pe...@harvardpilgrim.org]
Sent: Friday, August 07, 2015 3:22 PM
To: Greenlee, Robert T PHD
Cc: Verhagen, Laurel A; Sturtevant,Jessica; Horgan,Casie
Subject: Site IBQ Readiness /Response Dates

Dear Robert,

My name is Lindsey Petro and I am a PCORnet Research Assistant who will be 
working alongside Jessica Sturtevant, Casie Horgan, and the HPHCI DSSNI team. I 
look forward to working with you and the entire GPC team as we move through 
this very exciting development process for PCORnet!

In reviewing IBQ submissions, we noted that the following sites have received 
and not yet responded, or have not yet received the initial basic query (IBQ). 
If any sites require technical assistance, please let us know. Could you please 
update with an expected readiness date for IBQ receipt?

DataMart Name

IBQ Submitted (Y/N)

IBQ Readiness/Response Date

C4 GPC (University of Kansas)

N



C4 GPC (University of Wisconsin Madison)

N



C4 GPC (Medical College of Wisconsin)

Y



C4 GPC (Children's Mercy Hospital)

Y



C4 GPC (University of Texas Southwestern Medical Center)


Y





Thank you in advance for your help and have an enjoyable weekend!

Best wishes,
Lindsey

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RE: #291: Gather 2015 2nd quarterly QA results

[Thomas Mish]

I've uploaded these partial results into the GPC REDCap, thanks.

-TM


From: Apathy,Nate [mailto:nate.apa...@cerner.com]
Sent: Wednesday, July 29, 2015 10:53 PM
To: Thomas Mish 
Cc: Fothergill, Rita ; Teachout, Warren, C 
(wcteach...@cmh.edu) ; Maples,Claire 

Subject: #291: Gather 2015 2nd quarterly QA results


Hi Tom,



Sorry for the delay on these QA numbers. For CMH, here are our updated overall 
counts:


Total enrollment

  233,634

Diagnoses

  222,736

Biophysiological data

  215,631

Prescription and pharmacy data

  151,210

Laboratory data

  119,881

Procedures

58,853

Vital records

  233,634




We're waiting on the Oracle version of the scripts for the Term Matching 
queries and PCORI+ reporting queries. I don't anticipate good "Term Matching" 
results since we have our ontologies aligned to the SCILHS ontology in 
anticipation of that transition. I'll try to grab our obesity QA counts before 
the end of the week to augment these.



Thanks,



Nate Apathy

Program Manager | nate.apa...@cerner.com<mailto:nate.apa...@cerner.com> | 
816.201.2785



-Original Message-
From: 
gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu> 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
Sent: Monday, July 27, 2015 4:50 PM
To: m...@wisc.edu<mailto:m...@wisc.edu>; 
b...@uthscsa.edu<mailto:b...@uthscsa.edu>; 
dconno...@kumc.edu<mailto:dconno...@kumc.edu>; 
ngra...@kumc.edu<mailto:ngra...@kumc.edu>; 
verhagen.lau...@mcrf.mfldclin.edu<mailto:verhagen.lau...@mcrf.mfldclin.edu>; 
jd...@umn.edu<mailto:jd...@umn.edu>
Cc: gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>
Subject: Re: [gpc-informatics] #291: Gather 2015 2nd quarterly QA results



#291: Gather 2015 2nd quarterly QA results

--+---

Reporter:  mish  |   Owner:  bos

 Type:  problem   |  Status:  assigned

Priority:  major |   Milestone:  data-quality-q2

Component:  data-quality  |  Resolution:

Keywords:|  Blocked By:  259, 281, 285, 290, 306, 309

Blocking:|

--+---



Comment (by mish):



Here are the results so far:



|| ||=Qa Base Results   =||=Qa Base Percentages =||=Qa Base Results=||= Qa

Base Percentages =||=Qa Bc Results   =||=Qa Ob Results

=||=Qa Base Results=||= Qa Base Percentages=||= Qa Bc Results=||=   Qa

Ob Results=||=   Qa Term Matching=||=Qa Pcori Report+||

|| ||=2014 Q4   =||=2014 Q4=||= 2015 Q1 =||=2015 Q1=||= 2015 Q1=||=

2015 Q1=||= 2015 Q2=||= 2015 Q2=||= 2015 Q2 =||=2015 Q2

=||=2015 Q2 =||=2015 Q2||

||CMH||X||X||X||X|| ||X|| || || || || ||  ||  ||KUMC||X||X||X||X||X||X|| || || 
|| || || ||  ||MCRF||X||X||X||X||X||X||X||X||X||X||X||X||

||MCW||X||X|| || || || || || || || || ||  ||  ||UIOWA||X||X|| || || || || || || 
|| || || ||  ||UMN||X||X||X||X||X||X||X||X||X||X||X||X||

||UNMC||X||X||X||X||X||X|| || || || || || ||  ||UTHSCSA||X||X||X||X||X||X|| || 
|| || || || ||  ||UTSW||X||X||X||X||X||X|| || || || || || ||  
||WISC||X||X||X||X||X||X||X||X||X||X||X||X||



I have heard from KUMC (Nathan) and they hope to have results in yet this  
week. I need to start the write up soon. Are there any other sites I  should 
wait for before starting (UTHSCSA perhaps??) This Friday is the  absolute 
latest for getting your data in before I start trying to draw  some conclusions.



--

Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/291#comment:20>

gpc-informatics <http://informatics.gpcnetwork.org/>

Greater Plains Network - Informatics

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FW: [gpc-informatics] #12: Teleconference records for gpc-dev weekly - 7/14/2015

[Thomas Mish]

The link to yesterday's 
minutes<https://docs.google.com/document/d/1DR1MSa752O5yT8lnGvkTiUVwzcZVnYTKVneN1FjxVhQ/edit?usp=sharing>
 can be found as a part of ticket 
#12<https://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:70>.



-TM





-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Wednesday, July 15, 2015 8:35 AM
To: dconno...@kumc.edu; jd...@umn.edu; ngra...@kumc.edu; 
verhagen.lau...@mcrf.mfldclin.edu; huhick...@nebraskamed.com; 
bo...@uthscsa.edu; b...@uthscsa.edu; Thomas Mish
Subject: Re: [gpc-informatics] #12: Teleconference records for gpc-dev weekly



#12: Teleconference records for gpc-dev weekly

---+---

Reporter:  dconnolly  |   Owner:  jdale

 Type:  task   |  Status:  assigned

Priority:  minor  |   Milestone:

Component:  data-stds  |  Resolution:

Keywords: |  Blocked By:

Blocking: |

---+---



Comment (by mish):



UTSW has volunteered for the 21st. Thanks Debbie/Angela for the combined  
efforts on the notes for this meeting.



*

[https://docs.google.com/document/d/1DR1MSa752O5yT8lnGvkTiUVwzcZVnYTKVneN1FjxVhQ/edit

gpc-dev 14-Jul 2015 google doc notes]



--

Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:70>

gpc-informatics <http://informatics.gpcnetwork.org/>

Greater Plains Network - Informatics
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Tentative Agenda for 2015-07-14 GPC DEV Meeting

[Thomas Mish]

Minutes have been started at: 14 July 2015 GPC Dev Meeting 
Notes


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

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

b.roll: all 10(12) 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, (MU), 
(IU)
Reminder - put institution after your name in GoToMeeting preferences

c.today's scribe: Debbie@WISC. comments on the agenda? on last week’s notes 
(#12)?
recent tickets opened/closed FYI (note also recent ticket comments 
report):

d.Next Meeting: July 21, Dan should be back unless he enjoys vacation too 
much.

  i.We need a volunteer scribe for 
the 21st

2.Action Needed - PCORI Phase 2 
Survey   
Brittany Zschoche

.This is finished?

3.Review of current work by owner 
site. What else is 
your site working on for GPC?

4.milestone:data-quality-q2

.#291 Gather 2015 2nd quarterly QA 
numbers –

1.UTHSCSA

2.MCRF

3.Iowa

4.UMN

5.ETA for running at all sites?

Tom - give us 2 more weeks for ALL sites to run it and then 1 more week for Tom 
to compile the results




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RE: Babel updates

[Thomas Mish]

I'd vote for this being something of interest. We've be reengineering our build 
process and would love to be able to automate more of it.

-TM

-Original Message-
From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Hickman, Hubert B
Sent: Tuesday, May 26, 2015 10:10 AM
To: gpc-dev@listserv.kumc.edu
Subject: Babel updates

I've finally spent some development/brain cycles working on automating our 
babel updates here at UNMC.  It now  takes about 2.5 minutes for our babel 
update to happen now - using some of the same ideas used to move our Oracle 
data into Postgresql to construct the new identified warehouse.   I have shell 
access to babel, so I may have some options that other places do not, but I 
think my code could be used by other sites (or perhaps others have the process 
well honed already, and I am trailing the pack here).  The code exports the 
metadata, copies it to  babel, and generates and executes the update statements 
for babel's table_access table.

If it is of interest, I'll put something up on bitbucket or elephant.

Hubert Hickman
Systems Sr. Analyst
huhick...@nebraskamed.com
(402) 559-4838



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