CDM refresh

[Gryzlak, Brian M]

Can someone confirm that there is a CDM refresh due 10/16 and if so is there 
guidance available?  For example, will this be submitted as a query through the 
DataMart Client?

Thanks,
Brian


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

[GPC Informatics]

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  campbell
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:  411  |
-+

Comment (by dconnolly):

 Thanks, Jay and UNMC folks. Those 478,729 NDC codes cover 99% of the ~200M
 medication facts in grouse.

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

[GPC Informatics]

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  campbell
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:  all-sites|  Blocked By:  568, 592
 Blocking:  411  |
-+

Comment (by jay.pedersen):

 The link to the zip file of SCILHS MEDICATION metadata from comment 26 is
 no longer valid.  The following is the current link:

 https://www.dropbox.com/s/oc56lvqi7jvftp8/scilhs_meds_mods.zip?dl=0

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Re: [gpc-informatics] #625: Disk space allocation and LVM setup for SNOW SHRINE spoke server(s)

[GPC Informatics]

#625: Disk space allocation and LVM setup for SNOW SHRINE spoke server(s)
--+
 Reporter:  kwanta|   Owner:  kwanta
 Type:  task  |  Status:  new
 Priority:  critical  |   Milestone:  snow-shrine-2
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:
 Blocking:|
--+

Comment (by hangs008):

 Replying to [comment:6 manuells]:
 > UTHSCSA:
 > We're short on hardware here and only have 8.5GB for the Snow Shrine
 server. UMN any way you guys can share your scripts for the compression
 and alerts? We will likely need something like that. Thanks!

 Our ops team uses zabbix and splunk to handle most things like this. If
 you need an easy way to compress your i2b2 logs you could set up a cron
 job to run
 {{{
 gzip /path/to/i2b2/logs/*.log.*
 }}}
 which would handle the logs that are automatically rotated out by
 jboss/wildfly. We disabled most of the console logging for jboss/wildfly
 so our console.log in /var/log/jboss-as doesn't get too large. If you
 needed to rotate that you could probably do something like
 {{{
 mv /var/log/jboss-as/console.log /var/log/jboss-as "console.log.$(date
 +%s)"
 touch /var/log/jboss-as/console.log
 gzip /var/log/jboss-as/console.log.*
 }}}
 gzip will automatically skip any files that are already gzipped so it
 saves some of the extra scripting work.

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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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RE: Standardizing Note Types LOINC document-ontology option?

[Russ Waitman]

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.

[cid:image001.png@01D33694.D1608620]@djvreeman

[cid:image002.png@01D33694.D1608620]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
https://docs.google.com/document/d/1MFWLqzMfuGQfroJRqOpCHZk93RD-VvwZ3rWzFJuQnwc/edit
https://informatics.gpcnetwork.org/trac/Project/ticket/431

that LOINC has this
https://loinc.org/document-ontology/ with 5 dimensions and is supposedly “used 
worldwide in HL7's CDA standard”.

Ideally there would be a relationship somewhere in Cerner, Cattails, and Epic 
that let’s us crosswalk our note titles authored in that EHR or blowing in from 
ancillaries or other systems that do link to this LOINC ontology coding scheme 
that on cursory glance might somehow be coded when the documents go outbound as 
a CDA.
http://www.hl7.org/implement/standards/product_brief.cfm?product_id=379

See Kris’ work in  https://informatics.gpcnetwork.org/trac/Project/ticket/573 
and the note type volumes sorted 
https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/573/Note%20Types%20by%20Encounter%20Type.xlsx
 ).

An example would be a physician writing a history and physical in a nursing 
facility
34116-4

LP173418-7

Document.Kind

1

Note

34116-4

LP173198-5

Document.TypeOfService

1

History and physical

34116-4

LP173048-2

Document.Setting

1

Nursing facility

34116-4

LP173084-7

Document.Role

1

Physician


And then it seems there are separate mappings to the Subject Matter Domain.

Otherwise, the work to map to the five dimensional ontology is possible but 
non-trivial because some info is in the title but others in the author and 
location which may be hard to determine as least at my first 15 minute glance.

Jim Campbell/Scott Campbell/Jim McClay at Nebraska may be already in this space 
based on their HL7 and lab/path work.

Others from the Regenstrief group may know who’s doing this best nationally or 
if the bread crumb is there somewhere for at least certain note types.

Russ Waitman, PhD
Director of Medical Informatics
Associate Vice Chancellor for Enterprise Analytics
Professor, Department of Internal Medicine
University of Kansas Medical Center, Kansas City, Kansas
913-945-7087 (office)
rwait...@kumc.edu
http://www.kumc.edu/ea-mi/
http://informatics.kumc.edu
http://www.gpcnetwork.org – a PCORnet collaborative 
www.pcornet.org