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

___
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev

Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  minor |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-
Changes (by dconnolly):

 * cc: ngraham, bzschoche, gpc-dev@… (removed)
 * priority:  major => minor


Comment:

 Replying to [comment:32 meiliu]:
 > Bernie replied on 9/13 at 9:57AM with the following:
 > October would be good if feasible. ... We will circulate ... details on
 the data pull in the next couple of days.

 Since that didn't work out, October isn't a good bet.

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
___
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev

Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by dconnolly):

 Regarding the data requested for 5 Sep (comment:23): Now that we have data
 from a critical mass of sites (UIOWA, MCW, UTSW, IU, KUMC), let's track
 the others separately:

  - MU #641
  - UNMC #642
  - UMN #643

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
___
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev

Re: Standardizing Note Types LOINC document-ontology option?

[Genevieve Melton-Meaux]

Sorry for the late reply on this. Have included our main collaborator, Liz Chen 
at Brown, on the thread.

Yes - our original experience with this is somewhat dated but rooted in work 
with Sue Bakken at Columbia looking at HL7-LOINC DO as a clinical document 
representation tool overall and evaluating the SMD (Subject Matter Domain) axis 
for the DO. 

Most recently, we have done the following: 
Mapped the UMN CDR documents and associated document metadata to the DO 
 
Took the two Axes with most coverage gaps (Settings of Care 
 and Role 
) and proposed comprehensive 
value sets based off of associated standards 
Unaware if these valuesets which are available as resources are part of the new 
HL7-LOINC DO release. 

Link: https://healthinformatics.umn.edu/research/nlpie-group/nlpie-resources

Please reach out to Liz and I with any specific questions.

GMM

Genevieve Melton-Meaux, MD, PhD
Professor of Surgery and Health Informatics Core Faculty 
University of Minnesota
Chief Data and Health Informatics Officer 
Fairview Health Services 
Email: gmel...@umn.edu ; Cell - 612-790-0401 
; Pager - 612-899-6222 

Informatics research - Elizabeth Lindemann (linde...@umn.edu 
) 612-625-4377 

The information transmitted in this e-mail is intended only for the person or 
entity to which it is addressed and may contain confidential and/or privileged 
material, including "protected health information." If you are not the intended 
recipient, you are hereby notified that any review, retransmission, 
dissemination, distribution, or copying of this message is strictly prohibited. 
If you have received this communication in error, please destroy and delete 
this message from any computer and contact us immediately by return e-mail.

> On Sep 26, 2017, at 7:27 AM, Russ Waitman  wrote:
> 
> Hi Dan,
> Thank you for pointing out those references and I see that Genevieve 
> Melton-Meaux has been involved in several of your referenced papers.  It 
> seems that the most recent article found the LOINC DO was inadequate.  Did 
> the Minnesota team follow up with the LOINC team wrt that finding?  Since 
> it’s from 2015 and the new release is this year, I don’t know if the concern 
> has been addressed.
>  
> Pragmatically, many of the note templates IDs are common across epic sites so 
> if we could coordinate subject matter/role/location out of Clarity we can see 
> how close people could get to mapping 100s of millions and perhaps over a 
> billion notes in the GPC to this ontology.
>  
> Also didn’t know if now that you’re up on Epic, whether Paul Dexter or 
> whoever is point for notes at Regenstrief has done this at Eskenazi,
>  
> Russ
>  
> From: Daniel Vreeman [mailto:dvree...@regenstrief.org 
> ] 
> Sent: Wednesday, September 20, 2017 4:03 PM
> To: Russ Waitman
> Cc: GPC-DEV@LISTSERV.KUMC.EDU ; Allen, 
> Katie; stan.h...@imail.org ; dr...@epic.com 
> ; Zabriskie, Mary; Abhyankar, Swapna; Finnell, John T
> Subject: Re: Standardizing Note Types LOINC document-ontology option?
>  
> Hi Russ -
> 
> Thanks for highlighting this important area of LOINC. There are quite a few 
> papers describing use of the ontology that we link to on the LOINC site 
> . One other elaboration...
> 
> The VA and DoD have been keenly interested in the development of the LOINC 
> Document Ontology over its 15+ year history. In addition to the documentation 
> and content we publish from LOINC, you might also be interested in the HL7 
> Implementation Guide: LOINC Document Ontology, Release 1 
> . 
> This guide was stimulated by the interest in interoperability between DoD/VA 
> and describes how you might use the DO framework and attributes to facilitate 
> cross-organizational searches for documents, etc.
> 
> 
> Thanks,
> 
> Daniel J. Vreeman, PT, DPT, MS
>  
> Director, LOINC and Health Data Standards Regenstrief Center for Biomedical 
> Informatics
> Regenstrief-McDonald Scholar in Data Standards Indiana University School of 
> Medicine
> Research Scientist Regenstrief Institute, Inc.
> @djvreeman   
> loinc.org 
> 
> 
> Russ Waitman wrote:
> 
> Hi GPC-DEV,
> I had to drop off the call to make a LOINC equivalence group call led by our 
> colleagues at Indiana (Dan Vreeman and Katie Allen).
> https://loinc.org/groups/ 
>  
> As that call developed I then learned relevant to our discussion today of how 
> to manage different note types across GPC sites
>