Re: [gpc-informatics] #254: prepare Weight and Health survey contact information at all sites

[GPC Informatics]

#254: prepare Weight and Health survey contact information at all sites
+-
 Reporter:  sschlacter  |   Owner:  bzschoche
 Type:  task|  Status:  assigned
 Priority:  major   |   Milestone:  obesity-survey-def
Component:  data-sharing|  Resolution:
 Keywords:  obesity-cohort  |  Blocked By:  249, 250, 252, 253
 Blocking:  379 |
+-

Comment (by dconnolly):

 Dan Hale gave an update as of Sep 25 at
 [http://www.gpcnetwork.org/?q=LEK2015 the LEC]:
   1. **CMH: Pending** (no surveys sent)
   2. MCRF: collecting responses
   3. **UIOWA: Pending**
   4. KUMC: Done (all responses collected)
   5. MCW: collecting
   6. **UNMC: Pending**
   7. **UMN: Pending**
   8. UTSW: collecting
   9. UTHSCSA: Done
   10. **WISC: Pending**

 He asked how much longer we should allow before we proceed without the
 remaining sites, suggesting the end of October as the last date to begin
 collecting.

--
Ticket URL: 

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Re: gpc-dev 6 Oct agenda and meeting notes

[Justin Dale]

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  wrote:

> What else for tomorrow?
>
> shared notes for Oct 6
> ;
> current snapshot:
>
> --
>
>
>1.
>
>Convene, take roll, review records and plan next meeting
>1.
>
>   ​Meeting ID and access code: 817-393-381
>   ; call +1
>   (571) 317-3131
>   2.
>
>   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
>   1.
>
>  today's scribe: KUMC
>  3.
>
>   comments on the agenda? on last week’s notes (#12
>   )? recent
>   tickets
>   opened/closed
>    FYI
>   (note also recent ticket comments report
>   ):
>   1.
>
>  #367 (update KUMC babel terms w.r.t ICD10) closed
>  
> 
>  1.
>
> #375 (KUMC Babel terms lack "KUMC" prefix on tooltips
> 
> 
> 2.
>
>  #376 (data builder limited to `like
>  concept_dimension.concept_path` metadata) created
>  
>  3.
>
>  #370 (compresed file upload for use in babel DB IDE) reopened
>  
> 
>  4.
>
>  #378 (Estimate maximum cohort size from KUMC for CMS/Duke
>  collaboration) closed
>  
> 
>  5.
>
>  #178 (determine whether last.visit is the last fulfilled visit
>  or the last ...) closed
>  
> 
>  4.
>
>   Next Meeting: 13 October Scribe Volunteer?
>   2.
>
>#377 (Distribute Social Security Death Master file to sites) created
>
>3.
>
>milestone:geocode-1
>
>1.
>
>   #350  
> geocoding:
>   distribute census, ACS data to sites
>   
>   1.
>
>  Van Riper Oct 2: “I will work with Justin Dale at the UMN CTSI
>  to get you access to your data via SFTP”
>  4.
>
>milestone:data-domains3
>,
>drn-query-1
>
>1.
>
>   #160  
> reproducible
>   GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4)
>   
>   2.
>
>   DRN status at GPC sites
>   
> 
>   5.
>
>milestone:cohort-char-als
>
>1.
>
>   #380 (Collect ALS survey data, EMR data from participating sites)
>   created 
>   blocked by…
>   2.
>
>   #284  Deploy
>   GPC ALS Survey at GPC sites
>   
>   6.
>
>

gpc-dev 6 Oct agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

shared notes for Oct 
6;
 current snapshot:




  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 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 
(note also recent ticket comments 
report):

*   #367 (update KUMC babel terms w.r.t ICD10) 
closed

   *   #375 (KUMC Babel terms lack "KUMC" prefix on tooltips 


*   #376 (data builder limited to `like concept_dimension.concept_path` 
metadata) created

*   #370 (compresed file upload for use in babel DB IDE) 
reopened

*   #378 (Estimate maximum cohort size from KUMC for CMS/Duke 
collaboration) 
closed

*   #178 (determine whether last.visit is the last fulfilled visit or 
the last ...) 
closed

 *   Next Meeting: 13 October Scribe Volunteer?

  2.  #377 (Distribute Social Security Death Master file to sites) 
created

  3.  
milestone:geocode-1

 *   #350 
geocoding: distribute census, ACS data to 
sites

*   Van Riper Oct 2: “I will work with Justin Dale at the UMN CTSI to 
get you access to your data via SFTP”

  4.  
milestone:data-domains3,
 
drn-query-1

 *   #160 
reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 
2.4)

 *   DRN status at GPC 
sites

  5.  
milestone:cohort-char-als

 *   #380 (Collect ALS survey data, EMR data from participating sites) 
created blocked by…

 *   #284 
Deploy GPC ALS Survey at GPC 
sites

  6.  
milestone:cohort-char1

 *   #138 (top labs, meds, procedures query, plug-in) 
closed - 
ref chinotype

 *   #228 (DataBuilder output not directly analyzable) closed 
 - ref 
datafinisher, edc_summary, etc.

 *   #379 (Link EHR data to Health and Medical Research Family Survey 
(HMRFS) 2 ...) 
created blocked by …

 *   #254 
prepare Weight and Health survey contact information at all 
sites

  7.  
milestone:cms-resdac-etl

 *   #287 (Search ResDAC synthetic claims data for ICD9 diagnoses in 
development i2b2 ...) 
closed

*   #316 (All 10 DX from Inpatient, outpatient, carrier tables) 
closed

 *   #314 (Query by CMS beneficiary demographics) closed by 
dconnolly

 *   #336 (Search ResDAC synthetic claims data (diagnoses, demographics) on 

RE: [gpc-informatics] #243: GPC Procedure Ontology: CPT, HCPCS

[Dan Connolly]

The SCILHS ontology has both CPT and HCPCS, no?

-- 
Dan


From: Phillip Reeder [phillip.ree...@utsouthwestern.edu]
Sent: Monday, October 05, 2015 9:07 AM
To: gpc-dev@listserv.kumc.edu; Dan Connolly; b...@uthscsa.edu; m...@wisc.edu; 
nate.apa...@cerner.com
Subject: Re: [gpc-informatics] #243: GPC Procedure Ontology: CPT, HCPCS

I¹d be curious to see what sort of coverage people are getting with the
Harvard HCPCS terminology. San Antonio¹s terminology looks to have more
stuff in it.   For example, HCPCS Level 2 has 282K facts, which I think is
what is built out in the PCORnet terminology, vs. 2.8M facts for the CPT
hierarchy.

Phillip

On 10/2/15, 9:22 AM, "GPC Informatics"  wrote:

>#243: GPC Procedure Ontology: CPT, HCPCS
>--+
> Reporter:  dconnolly |   Owner:  bos
> Type:  design-issue  |  Status:  assigned
> Priority:  major |   Milestone:  data-domains3
>Component:  data-stds |  Resolution:
> Keywords:|  Blocked By:
> Blocking:|
>--+
>
>Comment (by dconnolly):
>
> The
>
>[https://community.i2b2.org/wiki/display/SCILHS/SCILHS+i2b2+PCORnet+Common
>+Data+Model+Ontology+Home
> SCILHS ontology] provides another candidate (see also
> ticket:191#comment:3).
>
> Version 1.5.2 is on [https://babel.gpcnetwork.org/ babel] as "PCORnet
> Procedures"; for example, HCPCS J codes:
>
> {{{
> 3
> \\PCORI_PROC\PCORI\PROCEDURE\HC\J9010-J\
> J9010 - J: Chemotherapy Drugs
> \PCORI\PROCEDURE\HC\J9010-J\
> HCPCS \ Chemotherapy Drugs
> }}}
>
>--
>Ticket URL:
>
>gpc-informatics 
>Greater Plains Network - Informatics
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UT Southwestern


Medical Center



The future of medicine, today.


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Re: [gpc-informatics] #160: reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4)

[GPC Informatics]

#160: reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO
milestone 2.4)
-+--
 Reporter:  rwaitman |   Owner:  prakashnadkarni
 Type:  enhancement  |  Status:  assigned
 Priority:  minor|   Milestone:  data-domains3
Component:  data-stds|  Resolution:
 Keywords:  cdm; enrollment  |  Blocked By:  145
 Blocking:   |
-+--
Changes (by dconnolly):

 * owner:  dconnolly => prakashnadkarni
 * status:  reopened => assigned


Comment:

 I our 29 Sep call (#12), Prakash offered to share code for his approach to
 CDM ETL.

--
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Re: [gpc-informatics] #327: Gather 2015 3rd quarterly QA results

[GPC Informatics]

#327: Gather 2015 3rd quarterly QA results
--+--
 Reporter:  mish  |   Owner:  mish
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-q3
Component:  data-quality  |  Resolution:
 Keywords:|  Blocked By:  309, 351, 366
 Blocking:|
--+--

Comment (by dconnolly):

 If anyone is willing to lead this while Tom is on holiday, please let me
 know.

--
Ticket URL: 

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Re: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit

[GPC Informatics]

#178: determine whether last.visit is the last fulfilled visit or the last
scheduled visit
-+---
 Reporter:  mish |   Owner:  dconnolly
 Type:  enhancement  |  Status:  closed
 Priority:  minor|   Milestone:  cohort-char1
Component:  data-stds|  Resolution:  invalid
 Keywords:   |  Blocked By:
 Blocking:   |
-+---
Changes (by dconnolly):

 * status:  assigned => closed
 * resolution:   => invalid


Comment:

 Since our BC finder file QA (#227) is done, this is overtaken by events.

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