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

[Nathan Graham]

Jeff/All,

It looks like we were missing an index on the UNMC table - try now?  Initial 
manual testing shows that it's a lot faster (the UNMC hierarchy anyway).

See also https://informatics.gpcnetwork.org/trac/Project/ticket/568#comment:11.

--
Nathan

-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Klann, 
Jeffrey G.
Sent: Wednesday, April 12, 2017 3:36 PM
To: Campbell, James R; gpc-dev@listserv.kumc.edu; Pedersen, Jay G; 
huhick...@nebraskamed.com; Dan Connolly; Russ Waitman
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Great, I see that Dan opened a ticket about BABELing. Not sure where you’re 
pushing it but please let me know when you have and we’ll be glad to take a 
look. 

It looks like you are using ATC, not NDF-RT (VA)?

Also, if you are including all retired RxNorm codes, how do you arrange the 
ontology in the case where two RxNorm codes refer to exactly the same drug?

Thanks,
Jeff Klann, PhD

On 4/12/17, 9:46 AM, "Campbell, James R"  wrote:

Jeff
I assume you are trying to review on BABEL?  I will leave indexing and 
efficiency there to KU's discretion.

Jay is pushing a copy along with documentation up to your GITHUB site for 
you and the SCILHS community to comment.  We have set the procedures and 
software arranged with NLM and we will take responsibility for refreshing the 
metadata every six months for SCILHS (and GPC) if you approve.  The VA/class 
top level ontology is basically what you have done with the minor exception of 
renaming some of the ingredient level nodes where the VA has not deployed all 
formulations of that ingredient class (like CARDIOVASCULAR -BETA BLOCKERS- 
TIMOLOL  where the eye preps of timolol are not included as subtypes for 
searching.

The need to have a metadata set that would index all US drugs is the reason 
that we added the second alpha ingredient list.  Speaking with NLM, NO drug 
classification - ATC, VA or whatever -is inclusive of all US pharmacopoeia.  
Ken Mandl co-authored a paper with Olivier Bodenreider discussing that very 
issue.

I would be very interested in your thoughts about this metadata when you 
get a chance to review
Jim

-Original Message-
From: Klann, Jeffrey G. [mailto:jeff.kl...@mgh.harvard.edu]
Sent: Tuesday, April 11, 2017 10:37 PM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G ; 
Campbell, James R ; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by 
ingredient

It is *extremely* slow to browse. Can you check your indexes? I’d like to 
explore your hard work but it’s unusable right now.

( I tried a few random other trees and they were also unbrowsably-slow. Is 
there an epidemic of bad indexes on babel? )

Thanks,

Jeffrey Klann, PhD
Instructor of Medicine, Harvard Medical School Instructor in Investigation, 
Massachusetts General Hospital


On 4/11/17, 12:00 PM, "GPC Informatics"  wrote:

#280: Medication ontology orgainzed by ingredient
-+
 Reporter:  preeder  |   Owner:  jay.pedersen
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  snow-shrine-2
Component:  data-stds|  Resolution:
 Keywords:   |  Blocked By:
 Blocking:   |
-+

Comment (by dconnolly):

 Replying to [comment:19 campbell]:
 > SCILHS/Medication metadata issues addressed with load to BABEL 
toiday:

 Which folder has the updated medication metadata? is it **UNMC:
 Medications (UNMC)**?

 > • (therefore) with VA drug classes as sole top-level ontology, 
not
 all clinical formulations or packages can be deployed

 So this is a wholesale re-organization of the ontology?

 If you can share the code you used to build it, please do.

--
Ticket URL: 

gpc-informatics 
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RE: UNMC -- BABEL update issue, timing out when trying to send updated metadata (SCILHS medications metadata)

[Nathan Graham]

Jay,

We recently rebuilt babel to be within the KUMC VPC and it sounds like we don't 
have all the network issues worked out yet.  I suspect it'll take us at least a 
couple of days before we knew the path forward for self-service Babel updates.

While we work on that, I could try uploading your terms for you.  If you'd like 
me to try, I'll send you an invite for https://securefiles.kumc.edu which will 
allow you to transfer large files.  Our e-mail filters have been a bit 
aggressive recently so I'm concerned they won't come through via e-mail.

Thanks.

--
Nathan

From: Pedersen, Jay G [mailto:jay.peder...@unmc.edu]
Sent: Sunday, April 09, 2017 9:38 AM
To: gpc-dev@listserv.kumc.edu
Cc: Campbell, James R; Dan Connolly; Nathan Graham
Subject: UNMC -- BABEL update issue, timing out when trying to send updated 
metadata (SCILHS medications metadata)


Hi,



I am trying to upload UNMC's latest metadata to BABEL,

so that the GPC can examine the SCILHS Medications metadata

that we have created.  I have been able to update BABLE

as recently as January 2017.



I am currently receiving a "connection timeout" when I try

to copy our metadata to babel.gpcnetwork.org.



Who would I talk to about this?



For example, here is what I see when trying to use the ssh client to access 
BABEL:


ssh jpeder...@babel.gpcnetwork.org<mailto:jpeder...@babel.gpcnetwork.org>
ssh: connect to host babel.gpcnetwork.org port 22: Connection timed out

I get the same message when trying to "scp" the metadata to the machine,
for use in updating the Postgresql database containing the metadata.


scp unmc_terms.csv.gz 
jpeder...@babel.gpcnetwork.org:/home/jpedersen/unmc_terms.csv.gz<mailto:jpeder...@babel.gpcnetwork.org:/home/jpedersen/unmc_terms.csv.gz>
ssh: connect to host babel.gpcnetwork.org port 22: Connection timed out

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)

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How to debug i2b2 queries that fail due to missing concepts

[Nathan Graham]

All,

We have noticed that sometimes after our monthly i2b2 refresh past user queries 
don't run anymore - instead, the webclient displays "ERROR: ERROR".  Sometimes 
(but not always) this error message is because concepts that used to be in the 
concept dimension are now missing.  At KUMC, our monthly refresh can change 
parts of the concept hierarchy from month to month.

During the Hackathon, Eric Larose showed me that you can see which concepts 
were missing in a particular query by looking in the QT tables - see below (I 
verified with him that it's ok to forward to GPC-dev).

Thanks Eric!

--
Nathan


From: Larose, Eric R [mailto:larose.e...@mcrf.mfldclin.edu]
Sent: Wednesday, January 18, 2017 8:26 AM
To: Nathan Graham
Subject: Missing concept codes in QT tables
Importance: High

Let me know if this isn't what you were talking about last night.  This is what 
I ran into when I restructured some of our ontology paths.

SELECT TOP 1000 [RESULT_INSTANCE_ID]
  ,[QUERY_INSTANCE_ID]
  ,[RESULT_TYPE_ID]
  ,[SET_SIZE]
  ,[START_DATE]
  ,[END_DATE]
  ,[STATUS_TYPE_ID]
  ,[delete_flag]
  ,[message] -- Contains Text when concept is missing from the ontology
  ,[description]
  ,[REAL_SET_SIZE]
  ,[OBFUSC_METHOD]
  FROM [vdw_i2b2data_2].[dbo].[QT_QUERY_RESULT_INSTANCE]
  WHERE DATALENGTH(message) <> 0 -- This is a text datatype and not varchar so 
I can't just compare to <> ''

EXAMPLE VALUE:
Missing Concept in Ontology Cell :
[\\i2b2\i2b2\LP29693-6\LP29697-7\LP71800-4\54050-0\54051-8\24321-2\2160-0\]  
panel#-1
[\\i2b2\i2b2\Cohort\Phenotype\T2 Diabetes\]  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A12973319\A8340125\A8358103\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A12973319\A8341296\443.9\]  
panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\430\]  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\431\]  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345436\]  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345439\]  panel#-1
[\\i2b2\i2b2\Demographics\Age Static\60-69\65\]  panel#-1
[\\i2b2\i2b2\Demographics\Age Static\60-69\66\]  panel#-1
[\\i2b2\i2b2\Demographics\Age Static\60-69\67\]  panel#-1
[\\i2b2\i2b2\Demographics\Age Static\60-69\68\]  panel#-1
[\\i2b2\i2b2\Demographics\Age Static\60-69\69\]  panel#-1
[\\i2b2\i2b2\Demographics\Age Static\70-79\]  panel#-1
[\\i2b2\i2b2\Demographics\Age Static\80-89\]  panel#-1
[\\i2b2\i2b2\Demographics\Age Static\>89\]  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359307\A15573936\A8352361\A8340910\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359307\A15573936\A8352361\A8340911\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359307\A15573936\A8352361\A8359116\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359307\A15573936\A8352361\A8340912\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359307\A15573936\A8352361\A8340913\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359307\A15573936\A8352361\A8340914\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359307\A15573936\A8352361\A8340915\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359307\A15573936\A8352361\A8340916\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359307\A15573936\A8352361\A8343926\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359307\A15573936\A8352361\A8343927\]
  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8341282\A8352272\] 
 panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8341282\A8352270\] 
 panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8341282\A8358497\] 
 panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8341283\]  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\436\]  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345446\437.0\]  
panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345446\437.1\]  
panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345446\437.3\]  
panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345446\437.4\]  
panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345446\437.5\]  
panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345446\437.6\]  
panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345446\437.7\]  
panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345446\437.8\]  
panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345446\437.9\]  
panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8352249\A8345450\]  panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8360933\A8339687\A8377811\] 
 panel#-1
[\\i2b2\i2b2\Diagnoses\A18090800\A8359006\A8359014\A8360933\A8339687\A8377603\

PCORNet ETL ADD Data Providence for SSDMF

[Nathan Graham]

All,

Kristen at MCW asked for guidance on what to select in the ETL Annotated Data 
Dictionary as the data providence for the social security death master file 
(specifically, the data providence question for the CDM DEATH table).

I looked at the KUMC draft and it seems we at KU selected "National Death 
Index" (along with EHR of course) which seemed right at first glance.  However, 
I searched the web and found that the CDC has something called "National Death 
Index (NDI)" (http://www.cdc.gov/nchs/ndi/) which doesn't appear to be the same 
thing as the SSDMF.

I'd be interested in feedback from the group as to what the right choice is.  
Perhaps simply "Death Registry"?  The options are:

- EHR
- National Death Index
- State Death Records
- Death Registry
- Other
- Not populated at this time

Regards,

Nathan
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RE: SCILHS i2b2 to CDM on Oracle

[Nathan Graham]

Phillip,

I've started hacking on the SCILHS->CDM 
code (I 
forked the SCILHS repositories on 
github/njgraham).  I think I'm seeing the same 
race vs. ethnicity issue you logged (Ethnicity issue 
#1).  See comment in 
PCORNetLoader_ora.sql, around line 
800.

Anyway, most of my changes thus far have been stubs, etc. to just get the code 
running but I've tried to add TODOs/comments as I go.  I suspect some of the 
TODOs may turn in to issues I log and others I'll remove as I figure out what's 
going on.

Have you ended up making more changes than you noted in the thread below?  Do 
you have your changes shared somewhere?

Thanks!

Regards,

Nathan


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, February 15, 2016 12:37 PM
To: Phillip Reeder; gpc-dev@listserv.kumc.edu
Subject: IN / LIKE limitation RE: SCILHS i2b2 to CDM on Oracle

Re IN / LIKE #2, would you please open an i2p-transform 
issue?

--
Dan

From: 
gpc-dev-boun...@listserv.kumc.edu 
[gpc-dev-boun...@listserv.kumc.edu] on behalf of Phillip Reeder 
[phillip.ree...@utsouthwestern.edu]
Sent: Wednesday, February 10, 2016 12:12 PM
To: gpc-dev@listserv.kumc.edu
Subject: SCILHS i2b2 to CDM on Oracle
Has anyone else attempted the SCILHS i2b2 to CDM code on Oracle?  I'm focusing 
on the demographics table to start with have run into a few things I wanted to 
share.

#1)  SCILHS relies on the patient_dimension for the demographics, not the 
observation_fact.  Just something to be aware of, not really a problem as long 
as you have the patient_dimension built out.
#2)  The demographics ontology has some rows that use the IN for the operator 
and some rows that use like.  But the code only works for the race/sex where it 
is using "IN" as the operator.  I added a where race.c_operator='IN' , 
sex.c_operator='IN' , hisp.c_operator='IN' where necessary to avoid the oracle 
error.
#3) For Hispanic, the code is only looking at the race_cd.  This only give you 
'Yes' or 'No-Information' as values.   I think it would make more sense to move 
the ethnicity information to an ethnicity_cd column.

Anyone else working with the i2b2 to CDM on Oracle code?  Just wondering if 
there are any other changes you've had to make to get it working.

Thanks,
Phillip





UT Southwestern


Medical Center



The future of medicine, today.


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RE: Agenda for today's call?

[Nathan Graham]

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] 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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RE: Babel

[Nathan Graham]

Tony,

Babel is working again.

The JBoss logs (Jan 13 16:29 server.log) said:

00:38:38,527 INFO  [org.apache.axis2.transport.http.HTTPSender] (Thread-36011) 
Unable to sendViaPost to 
url[http://localhost:9090/i2b2/services/OntologyService/getTermInfo]: 
java.net.SocketTimeoutException: Read timed out

I just restarted JBoss this time – I’d consider investigating root cause if we 
determine this isn’t just an isolated event.

Regards,

--
Nathan


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of French, Tony
Sent: Wednesday, January 13, 2016 10:09 AM
To: gpc-dev@listserv.kumc.edu
Subject: Babel


We are able to login to Babel (i2b2) but are not seeing any of the ontologies.  
Not a big deal at the moement but wanted to make sure the KUMC folks are aware 
if they aren’t else wise performing maintenance.


Thanks,
Tony



Tony French  |  Systems Engineer  - RPG Team Lead

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1101 West Tenth Street
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Tel 317-274-9087
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elephant.gpcnetwork.org is back up!

[Nathan Graham]

Elephant is back up!  Please commence pushing all that new wonderful code!

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Nathan Graham
Sent: Monday, December 14, 2015 3:58 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Subject: Elephant is currently down - KUMC is investigating

All,

elephant.gpcnetwork.org is currently down - we (KUMC) are investigating.  If 
you don't know what elephant.gpcnetwork.org is used for and are interested to 
find out, see 
MultiSiteDev<https://informatics.gpcnetwork.org/trac/Project/wiki/MultiSiteDev>.

For those of us at KUMC, work is being tracked in ticket #3912 (non-public).

Regards,

Nathan
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Elephant is currently down - KUMC is investigating

[Nathan Graham]

All,

elephant.gpcnetwork.org is currently down - we (KUMC) are investigating.  If 
you don't know what elephant.gpcnetwork.org is used for and are interested to 
find out, see 
MultiSiteDev.

For those of us at KUMC, work is being tracked in ticket #3912 (non-public).

Regards,

Nathan
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RE: Babel upgrade plans: Possible brief downtime today

[Nathan Graham]

All,

Babelhttps://babel.gpcnetwork.org/ with i2b2 version 1.7.06 is now available! 
 If you notice any oddities such as overlapping panels or lack of response when 
pressing Run Query, try clearing your browser cache and reloading the page.

Thanks!

Regards,

Nathan


From: Nathan Graham
Sent: Thursday, August 27, 2015 11:20 AM
To: 'GPC-DEV@LISTSERV.KUMC.EDU'
Cc: Russ Waitman
Subject: Babel upgrade plans: Possible brief downtime today

All,

I believe the newly upgraded Babel image is ready to go live.  I plan to 
switch the DNS record to point to the newly upgraded image this afternoon.  
There may be a brief downtime (though I don't think there will be).

The specific bug I was aiming to fix was that the On or before option for 
temporal relationships was missing.  That option now appears in version 1.7.06 
(see GPC ticket 305 
comment:12https://informatics.gpcnetwork.org/trac/Project/ticket/305#comment:12).

I'll another e-mail to gpc-dev letting everyone know when the change is 
complete.

Regards,

Nathan

From: Nathan Graham
Sent: Thursday, August 20, 2015 1:52 PM
To: GPC-DEV@LISTSERV.KUMC.EDUmailto:GPC-DEV@LISTSERV.KUMC.EDU
Cc: Russ Waitman
Subject: Babel upgrade plans: please avoid changes beginning Friday, August 21st

All,

I plan to upgrade Babel to i2b2 1.7.06 to address temporal query issues (see 
GPC ticket 305https://informatics.gpcnetwork.org/trac/Project/ticket/305).  
There will be a brief downtime tomorrow morning, Friday, Auguest 21st while I 
clone the existing AWS virtual machine.  There will be a second brief downtime 
(that I will announce beforehand via gpc-dev) while I make the upgraded clone 
available to users.

Changes made to Babel (update to term tables, etc.) between the two down times 
won't be saved!  So, if possible, please avoid making changes to Babel until we 
announce that the upgrade is complete.  Alternatively, if you really want/need 
to make updates right away please let me know and I'll postpone the upgrade or 
help reinstate the changes on the new upgraded instance.

Thanks!

Regards,

Nathan


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GPC 2nd quarter QA design looks nice!

[Nathan Graham]

Tom/James,

I've just started working on running the GPC Q2 quality queries here at KUMC 
and wanted to say that the design looks pretty slick!  I really like having the 
concept paths, codes, etc. split out into their own xlsx/csv file that loads 
nicely into REDCap to begin with.  I think that'll make it a lot easier to port 
to various sites.

Now, on to actually gathering results...

Refs:

* WISC BitBucket: 
gpc-2015-q2-qa-fileshttps://bitbucket.org/jvanschyndle/gpc-2015-q2-qa-files

* My fork on BitBucket: 
gpc-2015-q2-qa-fileshttps://bitbucket.org/njgraham/gpc-2015-q2-qa-files

Regards,

Nathan
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RE: Jira ticket/workaround for backgrounded i2b2 queries that never return

[Nathan Graham]

Keith,

I thought it was Hubert at UNMC, but the GPC Dev Meeting Notes 14 July 
2015https://docs.google.com/document/d/1DR1MSa752O5yT8lnGvkTiUVwzcZVnYTKVneN1FjxVhQ/edit
 notes say UTSW - maybe both sites had issues.  Or, maybe I'm just not 
remembering correctly.

--
Nathan

From: Wanta Keith M [mailto:kwa...@uwhealth.org]
Sent: Wednesday, July 15, 2015 10:15 AM
To: Nathan Graham; GPC-DEV@LISTSERV.KUMC.EDU
Subject: RE: Jira ticket/workaround for backgrounded i2b2 queries that never 
return

Nathan, on the GPC call yesterday, do you recall which organization had this 
issue?  I can suggest the fix to Partners, but it seems like a slightly 
different issue.  I am just following up to confirm.

~Keith

From: 
gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Nathan Graham
Sent: Tuesday, July 14, 2015 11:43 AM
To: GPC-DEV@LISTSERV.KUMC.EDUmailto:GPC-DEV@LISTSERV.KUMC.EDU
Subject: Jira ticket/workaround for backgrounded i2b2 queries that never return

All,

As per the gpc-dev call today, please see Jira CORE issue 149: JDBC calls to 
interrupted threads throw 
sqlexceptionshttps://community.i2b2.org/jira/browse/CORE-149?jql=text%20~%20%22Interrupted%20attempting%20lock%22
 for work on long-running i2b2 queries that get stuck in a processing state 
and never return.  Note that you have to log in to the Jira system in order to 
see the ticket information - otherwise Jira reports No issues were found to 
match your search.

Michael Horvath said in the description:
 As a temporary fix, we've commented out the t.interrupt() call without any 
 ill effects.

Specifically, here's the text from the patch we applied at KUMC:

--- 
./i2b2_1704_orig/edu.harvard.i2b2.crc/src/server/edu/harvard/i2b2/crc/ejb/QueryManagerBeanUtil.java
 2014-11-06 15:48:08.0 -0600
+++ 
./i2b2_1704/edu.harvard.i2b2.crc/src/server/edu/harvard/i2b2/crc/ejb/QueryManagerBeanUtil.java
  2015-02-10 08:35:26.0 -0600
@@ -231,7 +231,7 @@
throw new I2B2Exception(Thread error while 
running CRC job 
, e);
} finally {
-   t.interrupt();
+   //t.interrupt();
//exec = null;
t = null;
}
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Jira ticket/workaround for backgrounded i2b2 queries that never return

[Nathan Graham]

All,

As per the gpc-dev call today, please see Jira CORE issue 149: JDBC calls to 
interrupted threads throw 
sqlexceptionshttps://community.i2b2.org/jira/browse/CORE-149?jql=text%20~%20%22Interrupted%20attempting%20lock%22
 for work on long-running i2b2 queries that get stuck in a processing state 
and never return.  Note that you have to log in to the Jira system in order to 
see the ticket information - otherwise Jira reports No issues were found to 
match your search.

Michael Horvath said in the description:
 As a temporary fix, we've commented out the t.interrupt() call without any 
 ill effects.

Specifically, here's the text from the patch we applied at KUMC:

--- 
./i2b2_1704_orig/edu.harvard.i2b2.crc/src/server/edu/harvard/i2b2/crc/ejb/QueryManagerBeanUtil.java
 2014-11-06 15:48:08.0 -0600
+++ 
./i2b2_1704/edu.harvard.i2b2.crc/src/server/edu/harvard/i2b2/crc/ejb/QueryManagerBeanUtil.java
  2015-02-10 08:35:26.0 -0600
@@ -231,7 +231,7 @@
throw new I2B2Exception(Thread error while 
running CRC job 
, e);
} finally {
-   t.interrupt();
+   //t.interrupt();
//exec = null;
t = null;
}
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RE: Action Needed - PCORI Phase 2 Survey

[Nathan Graham]

All,

For the KU response, I modified number of patients seen based on Maryan's 
comments.  I queried the CDM encounter table and used the definition of 
active patient we used Characterize enrollment for PCORI Milestone 
1.1https://informatics.gpcnetwork.org/trac/Project/ticket/97.
  2 visits in the 3 years where the visits are separated by greater than 30 
 days.

Then, I picked distinct patients we saw in the past year who were also 
considered active.  This dropped the number of patients seen in the past 
year by about 20% from when I just counted every encounter in the past year.

For reference:

with snapshot_date as (
  /* From CDM ETL config Jenkins job - when we ETL'd data from Epic*/
  select to_date('2015-05-12', '-MM-DD') dt from dual
  ),
pats_delta as (
  -- If only one visit, visit_delta_days will be 0
  select enc.patid, max(enc.admit_date) - min(enc.admit_date) visit_delta_days
from snapshot_date, pcornet_cdm.cdm_encounter enc
where enc.admit_date  add_months(snapshot_date.dt, -36)
group by enc.patid
),
enrolled as (
  select *
  from pats_delta
  where visit_delta_days  30
  )
select count(distinct enc.patid)
from snapshot_date, enrolled enrld
join pcornet_cdm.cdm_encounter enc on enc.patid = enrld.patid
where enc.admit_date between add_months(snapshot_date.dt, -12) and 
snapshot_date.dt
;


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Brittany Zschoche
Sent: Wednesday, July 08, 2015 2:40 PM
To: 'gpc-dev@listserv.kumc.edu'
Cc: 'Laura Fitzmaurice (lfitzmaur...@cmh.edu)'; 'prdex...@regenstrief.org'; 
'gary-rosent...@uiowa.edu'; 'Parker, Jerry C.'; 'm...@medicine.wisc.edu'; Steve 
Fennel; 'Umberto Tachinardi'
Subject: RE: Action Needed - PCORI Phase 2 Survey

All:

Thank you for your timely responses to the survey.  Today I received 
clarification from Maryan Zirkle; please see below.

Hi Russ/Brittany,
Please see my responses to your questions below:

Question: Do you have specific criteria to define seen? Does this include 
anything that generates clinical data?

Answer: This should include active patients at each site. Please provide a 
definition of what you consider an active patient (i.e. 2 clinical-data 
generating encounters within X years) when giving your response.

Question: Could you please provide examples of these populations?

Answer: 
https://help.pcori.org/hc/en-us/articles/202629114-What-priority-populations-does-PCORI-want-to-address-with-its-research-

Please see this link on the PCORI website for information on PCORI's 
populations of interest.

Question: Could you please provide context and definition of high quality data?

Answer: Data that has been queried for traditional data quality (DQ) checks 
within the site (health system, academic center, community hospital, etc.) 
Given this definition, we hope you also consult with the Coordinating Center to 
get their understanding of this measure.
Best,
Maryan


We will follow up individually with questions, if needed.

Thanks,

Brittany

From: Brittany Zschoche
Sent: Monday, July 06, 2015 10:36 AM
To: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Cc: Laura Fitzmaurice (lfitzmaur...@cmh.edumailto:lfitzmaur...@cmh.edu); 
gary-rosent...@uiowa.edumailto:gary-rosent...@uiowa.edu; Umberto Tachinardi; 
'm...@medicine.wisc.edu'; 'Parker, Jerry C.'; 'prdex...@regenstrief.org'
Subject: Action Needed - PCORI Phase 2 Survey

Hi, everyone.

Late last week, PCORI sent an information request to Dr. Waitman.  The 
additional information will assist PCORI in evaluating GPC's Phase 2 
application.  This evaluation will occur at the Executive Committee meeting 
later this month, therefore we do not have any flexibility with our due date, 
and it relates directly to Phase 2 funding.

We request that answers are submitted by COB Friday, July 10th, and absolutely 
no later than Sunday, July 12th.  To expedite the gathering of information, we 
have created a REDCap 
surveyhttps://redcap.gpcnetwork.org/surveys/?s=WF7TLPAXW7.

Please make note of the following:


-  Re: geographical overlap - answer with patient duplication in mind

-  Re: number of patients transformed into CDM - answer using the same 
process used for previous interim reports

-  Query and linkage support is budgeted into the Phase 2 GPC budget at 
a central level

-  I emailed PCORI this morning to seek further clarification on the 
following:

o   Re: Patients seen at this site.

*  Do you have specific criteria to define seen?

*  Does this include anything that generates clinical data?

o   Re: Population of high interest.

*  Could you please provide examples of these populations?

o   Re: High quality of data.

*  Could you please provide context and definition?

o   I will forward responses as soon as I have them

Please let me know if you have any questions.

Brittany Zschoche, MBA
Project Manager, Enterprise 

GPC billing diagnosis modifiers from Clarity: Primary admit diagnosis is line=1?

[Nathan Graham]

Phillip/Hubert/All,

I'm working to implement GPC billing modifiers at KUMC.  I'm aiming for what's 
in Babel under GPC: Diagnosis #63\Modifiers\Billing Diagnosis\ (screenshot 
attached).  It seems that what's there represents the latest GPC decision 
unless I'm missing part of the discussion.

I've been reviewing Diagnoses Modifiers for data attribution 
(#90)https://informatics.gpcnetwork.org/trac/Project/ticket/90 - thanks to 
guidance from Phillip and others I think I see where in Clarity to get the need 
data.  However, I did want to check on primary/non-primary diagnosis modifier 
for admit diagnosis.  Did you assume that when LINE = 1 in 
HSP_ACCT_ADMIT_DX that it's the primary admit diagnosis and that all other 
LINE values are non-primary?  For discharge diagnosis (from 
HSP_ACCT_DX_LIST) the Clarity Data Dictionary 2014 explicitly says this - 
LINE = 1 is primary and all others are non-primary.  But for admit, it 
doesn't say this explicitly.

Thanks for your help!

For reference, here's what I plan to do based on the ticket/e-mail discussion 
and the Clarity documentation to implement the diagnosis modifiers I see in 
Babel (screenshot attached).

Admit: HSP_ACCT_ADMIT_DX
- Primary/Non-Primary: Primary is `LINE` = 1 like for discharge?

Discharge: HSP_ACCT_DX_LIST
- Primary/Non-Primary: Primary is `LINE` = 1 - non-primary are the rest
- Present on admission: `FINAL_DX_POA_C` flag

Professional: `ARPB_TRANSACTIONS`
- Primary/Non-Primary: `PRIMARY_DX_ID` indicates the Primary diagnosis.  
`DX_TWO_ID`, `DX_THREE_ID`...`DX_SIX_ID` are non-primary.

Screenshot from Babel attached:
[cid:image001.png@01D0A299.78040610]

Thanks again!

Regards,

Nathan
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Updated enrollment numbers for May interim report by 5/22

[Nathan Graham]

All,

Steve Fennel is working on the May interim report and he's asked for updated 
enrollment numbers from each site.  We've been through this before and everyone 
submitted results via e-mail.  However, this time we've created a REDCap form 
for quarterly report enrollment 
statisticshttps://redcap.gpcnetwork.org/redcap_v6.2.2/index.php?pid=22.  
Please fill this out by May 22nd.

The past few times we've done this we've suggested using the script attached to 
Ticket #97: Characterize enrollment for PCORI Milestone 
1.1https://informatics.gpcnetwork.org/trac/Project/ticket/97 (with path 
tweaks for your site).  However, this time we should be able to answer at least 
some of the questions with CDM queries.  So, bonus points to anyone who does so.

I believe I got population numbers from the following people last time:

* University of Iowa: Prakash Nadkarni

* Medical College of Wisconsin: Brad Taylor

* Marshfield Clinic: Laurel Verhagen

* San Antonio: Alex Bokov

* Children's Mercy Hospital: Rita Fothergill

* University of Nebraska: Jason Lebsack

* University of Wisconsin - Madison: Tom Mish

* University of Texas Southwestern: Phillip Reeder

* University of Minnesota: Justin Dale

Thanks for your help!

Regards,

Nathan

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RE: diag constant file

[Nathan Graham]

Susan,

See 
constants.sqlhttps://bitbucket.org/gpcnetwork/gpc-pcornet-cdm/src/2b34bc7b71b13382b2cb697a10688fbc37f06c0d/constants.sql?at=default.

--
Nathan

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Susan Morrison
Sent: Monday, April 13, 2015 9:52 AM
To: Phillip Reeder; Dan Connolly
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: diag constant file




Dan,
I am building the diagnosis table for the CDM but I don't have the build 
process for file diag_constants file.  Phillip said It possibly came from KU?
Does anyone have history on this file?

Thanks
Susan Morrison
Database Analyst
Office of Academic Information Systems (AIS)
UT Southwestern Medical Center
6303 Forest Park.| Suite BP4.100 | Dallas, TX  75390-9106
214-648-4293
susan.morri...@utsouthwestern.edumailto:teresa.bos...@utsouthwestern.edu



From: Susan Morrison 
susan.morri...@utsouthwestern.edumailto:susan.morri...@utsouthwestern.edu
Date: Friday, April 10, 2015 at 3:35 PM
To: Phillip Reeder 
phillip.ree...@utsouthwestern.edumailto:phillip.ree...@utsouthwestern.edu
Subject: diag constant file

Hey, rebuilding the DX cdm.   Can you tell me where the diag_constant file is?

Thanks,
Susan Morrison
Database Analyst
Office of Academic Information Systems (AIS)
UT Southwestern Medical Center
6303 Forest Park.| Suite BP4.100 | Dallas, TX  75390-9106
214-648-4293
susan.morri...@utsouthwestern.edumailto:teresa.bos...@utsouthwestern.edu





UT Southwestern


Medical Center



The future of medicine, today.


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Due Monday, January 12th: Population characterization (parts A and B) for PCORNet LOI

[Nathan Graham]

All,

As we discussed in the GPC-dev call 
yesterdayhttp://listserv.kumc.edu/pipermail/gpc-dev/attachments/20150107/1a231dff/attachment-0001.pdf,
 we're working on PCORnet Phase 
2http://www.pcori.org/announcement/national-patient-centered-clinical-research-network-clinical-data-research-networks
 letter of intent (LOI).  Much like the quarterly updates we've provided to 
PCORI, the LOI document 
templatehttp://www.pcori.org/sites/default/files/PCORI-PFA-CDRN-LOI-Template.doc
 has a couple of sections with tables devoted to population characteristics:

* Part A: Population Overview

* Part B: Insurance Coverage Overview

Brittany sent out an e-mail to the site PIs on Friday (January 02, 2015) asking 
that each site fill in these sections (among others) by Tuesday, January 6th.  
However, as per GPC-dev meeting notes for January 6, 
2015http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20150107/1a231dff/attachment-0001.pdf,
 Dr. Waitman has extended the requested deadline to Monday January 12th (for 
the tables in sections A and B at least).

Please let us know right away who from each site will be the primary contact 
for providing numbers for the tables in parts A and B.  For the PCORI quarterly 
updates, I believe I got population numbers from the following people:

* University of Iowa: Prakash Nadkarni

* Medical College of Wisconsin: Brad Taylor

* Marshfield Clinic: Laurel Verhagen

* San Antonio: Alex Bokov

* Children's Mercy Hospital: Rita Fothergill

* University of Nebraska: Jason Lebsack

* University of Wisconsin - Madison: Tom Mish

* University of Texas Southwestern: Phillip Reeder

* University of Minnesota: Justin Dale

There's been some discussion regarding what Number of active patients with 
data in the EMR means.  After talking with Dr. Waitman yesterday I plan to use 
the same method we used to characterize enrollment for PCORI milestone 
1.1https://informatics.gpcnetwork.org/trac/Project/ticket/97:

The GPC will use a refined definition of enrollment based upon the criteria we 
used in our proposal...2 visits in the 3 years where the visits are separated 
by greater than 30 days

I also plan to use that number for active patients as the denominator for 
part B.

Thanks for your help!

Regards,

Nathan
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RE: Due Monday, January 12th: Population characterization (parts A and B) for PCORNet LOI

[Nathan Graham]

Debbie,

That's a good question - I somewhat arbitrarily picked one of the groups per 
patient (Oracle min() function on the ID number associated with the group).  
Maybe that's not a good approach - I'm open to other ideas.

--
Nathan

From: Debbie Yoshihara [mailto:dlyos...@wisc.edu]
Sent: Wednesday, January 07, 2015 10:56 AM
To: Nathan Graham; GPC-DEV@LISTSERV.KUMC.EDU; 'prakash-nadka...@uiowa.edu' 
(prakash-nadka...@uiowa.edu); 'btay...@mcw.edu' (btay...@mcw.edu); 
'verhagen.lau...@mcrf.mfldclin.edu' (verhagen.lau...@mcrf.mfldclin.edu); Alex 
Bokov (bo...@uthscsa.edu); Fothergill, Rita, R rfotherg...@cmh.edu 
(rfotherg...@cmh.edu); 'Jason Lebsack (jlebs...@nebraskamed.com)' 
(jlebs...@nebraskamed.com); Mish Thomas F (tm...@uwhealth.org); 
phillip.ree...@utsouthwestern.edu; Justin Dale (jd...@umn.edu)
Cc: Steve Fennel
Subject: Re: Due Monday, January 12th: Population characterization (parts A and 
B) for PCORNet LOI

Hi,

When I do my query for Part B: Insurance Coverage Overview, there are patients 
(25%) which are in multiple
groups: for example, Commercial and Medicare FFS.  How are other groups marking 
this?  I will get  100%
if I mark these individuals in both groups.  The effective date is the same, so 
I have no choice but to use both.

--- Debbie


On 1/7/2015 8:58 AM, Nathan Graham wrote:
All,

As we discussed in the GPC-dev call 
yesterdayhttp://listserv.kumc.edu/pipermail/gpc-dev/attachments/20150107/1a231dff/attachment-0001.pdf,
 we're working on PCORnet Phase 
2http://www.pcori.org/announcement/national-patient-centered-clinical-research-network-clinical-data-research-networks
 letter of intent (LOI).  Much like the quarterly updates we've provided to 
PCORI, the LOI document 
templatehttp://www.pcori.org/sites/default/files/PCORI-PFA-CDRN-LOI-Template.doc
 has a couple of sections with tables devoted to population characteristics:

* Part A: Population Overview

* Part B: Insurance Coverage Overview

Brittany sent out an e-mail to the site PIs on Friday (January 02, 2015) asking 
that each site fill in these sections (among others) by Tuesday, January 6th.  
However, as per GPC-dev meeting notes for January 6, 
2015http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20150107/1a231dff/attachment-0001.pdf,
 Dr. Waitman has extended the requested deadline to Monday January 12th (for 
the tables in sections A and B at least).

Please let us know right away who from each site will be the primary contact 
for providing numbers for the tables in parts A and B.  For the PCORI quarterly 
updates, I believe I got population numbers from the following people:

* University of Iowa: Prakash Nadkarni

* Medical College of Wisconsin: Brad Taylor

* Marshfield Clinic: Laurel Verhagen

* San Antonio: Alex Bokov

* Children's Mercy Hospital: Rita Fothergill

* University of Nebraska: Jason Lebsack

* University of Wisconsin - Madison: Tom Mish

* University of Texas Southwestern: Phillip Reeder

* University of Minnesota: Justin Dale

There's been some discussion regarding what Number of active patients with 
data in the EMR means.  After talking with Dr. Waitman yesterday I plan to use 
the same method we used to characterize enrollment for PCORI milestone 
1.1https://informatics.gpcnetwork.org/trac/Project/ticket/97:

The GPC will use a refined definition of enrollment based upon the criteria we 
used in our proposal...2 visits in the 3 years where the visits are separated 
by greater than 30 days

I also plan to use that number for active patients as the denominator for 
part B.

Thanks for your help!

Regards,

Nathan




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--

Debbie Yoshihara Informatics Specialist

SMPH-IT, Biomedical Informatics Services

School of Medicine and Public Health, UW-Madison

dlyos...@wisc.edumailto:dlyos...@wisc.edu

Tel:(608)263-5643
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gpc-dev meeting link

[Nathan Graham]

Connect info for gpc-dev 
teleconferenceshttp://informatics.gpcnetwork.org/trac/Project/wiki/SoftwareDev#MeetingsTeleconferences:
1. Please join my meeting.
https://global.gotomeeting.com/meeting/join/686845717
2. Use your microphone and speakers (VoIP) - a headset is recommended. Or, call 
in using your telephone.
United States (Toll-free): +1 (267) 507-0008
United States: +1 (267) 507-0008
Access Code: 686-845-717
Audio PIN: Shown after joining the meeting
Meeting ID:686-845-717

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RE: RxNorm metadata

[Nathan Graham]

We used the exclude modifiers table to remove the modifiers from things that 
didn't really need them like NO HOME MEDICATIONS, EMPTY CONTAINER, PLASTIC 
BAG, MISCELLANEOUS MEDICAL SUPPLY MISC, etc.  These are things we put 
directly under the top level Medications folder as we didn't know where else 
to put them.  Maybe it could be argued that some of these don't have much 
research value - I don't know.  But, many of these concepts had lots of 
patient/fact counts so we didn't want to just exclude them.  At least the NO 
HOME MEDICATIONS item was specifically discussed and deemed worth 
addinghttps://informatics.kumc.edu/work/ticket/1775.

Our (KUMC) general approach is bring in everything - that way, we can all can 
see what we have available.  If/when we find that things can be improved (based 
on user feedback, etc) we can do that later.

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Munns, Michael B
Sent: Monday, December 08, 2014 10:30 AM
To: gpc-dev@listserv.kumc.edu
Subject: FW: RxNorm metadata

We can put them on the mailing list.
We did end up creating an empty table for the manual curation, also a empty 
table for the exclude modifiers.

Michael Munns
Database Analyst
402-559-3821

From: Nathan Graham [mailto:ngra...@kumc.edu]
Sent: Monday, December 08, 2014 10:18 AM
To: Munns, Michael B
Subject: RE: RxNorm metadata

Michael,

I'd really like to keep these conversations on the 
gpc-devhttp://listserv.kumc.edu/pipermail/gpc-dev/ mailing list (sign up from 
 herehttp://listserv.kumc.edu/mailman/listinfo/gpc-dev).  If you have 
questions I think others will too.  And, I think we all benefit from as much 
collaboration as we can have.  Could we move future questions there?

I think what you want is an empty table right now.  The manual curation table 
is what it says - a place for you to manually specify parents for medications 
that we didn't link from Epic to RxNorm.  The documentation could probably be 
better - from the comment at the top of the file:

Notes about manual curation:
med_map_manual_curation is a table that maps a clarity medication ID to a parent
concept.  It is designed to be used for medications that we couldn't map to 
RxNORM
directly from information in Clarity (via GCN, NDC, etc). This parent could be a
VA class or an SCDF/SBDF.

The table has the following columns:
CLARITY_MEDICATION_ID - the id of the med without direct linkage to RxNORM
CLARITY_NAME (not used for mapping - just for eyeballing)
FACTS (not used for mapping - just for eyeballing)
PATIENTS (not used for mapping - just for eyeballing)
VA_NAME (not used for mapping - just for eyeballing)
VA_RXAUI - If we didn't map to an SDF AUI (below), the fall back on this one 
for VA class.
SDF_RXAUI - Map here if not null, otherwise fall back on the VA_RXAUI (above)
SDF_NAME (not used for mapping - just for eyeballing)

I know I've probably made KU-specific assumptions in the code that make porting 
difficult.  So, if you have improvements, suggestions, etc I'd be very happy to 
look at patches.  Or, if you start using the Elephant repository (see 
MultiSiteDevhttps://informatics.gpcnetwork.org/trac/Project/wiki/MultiSiteDev)
 you could commit directly to a branch and we could work together to merge your 
changes into default as appropriate.

Thanks.

Regards,

Nathan


From: Munns, Michael B [mailto:mike.mu...@unmc.edu]
Sent: Thursday, December 04, 2014 4:18 PM
To: Nathan Graham
Subject: RE: RxNorm metadata
Importance: High

I have more questions about this rxnorm_terms table.

On line 274 there is a create the I am running as an insert, that contains a 
union for the manual curation. If I am following all of this correct, and I am 
not sure that I am,  some of this may be that it's the first time we've ran and 
the rxnorm_terms is empty.

To start though there is a view mapped_meds , that uses rxnorm_terms. Then the 
view unmapped_meds is built off of mapped_meds. The unmapped_meds view is used 
in a query to create the med_map_manual_curation.csv which is used to
Populate the med_map_manual_curation table.

The union in the create @274 calls the med_map_manual_curation table , which 
does not exist. The join is where its med id is not null. So I could remove 
that section of the code or put an empty table out there.

Any downside to an empty table or skipping that union you are aware of? Am I 
missing something?



Michael Munns
Database Analyst
402-559-3821

From: Munns, Michael B
Sent: Thursday, December 04, 2014 1:41 PM
To: 'Nathan Graham'
Subject: RE: RxNorm metadata

Nathan, I found it there and created the view.

There may be more questions coming though.

Michael Munns
Database Analyst
402-559-3821

From: Nathan Graham [mailto:ngra...@kumc.edu]
Sent: Thursday, December 04, 2014 11:04 AM
To: Munns, Michael B
Subject: RE: RxNorm metadata

Michael,

Normal_concept is created in 
metadata_init.sqlhttps://informatics.kumc.edu/work/browser/heron_load/metadata_init.sql

RE: RxNorm metadata

[Nathan Graham]

Michael,

I think you're looking at obsolete code (well, obsolete with respect to the 
current KUMC ETL code anyway).  The medication mapping code was recently 
rewrittenhttp://listserv.kumc.edu/pipermail/gpc-dev/2014q4/000655.html and 
the part you asked about was removed.

The main design change implemented during the rewrite was the paths/full names 
are comprised of the RxNorm AUIs/local medication IDs (for example, 
\i2b2\Medications\RXAUI:3257490\RXAUI:3257495\MEDICATION_ID:129272\).  As far 
as I know we plan to use the AUI-based paths as the GPC standard for 
medications (see also gpc-dev conference call notes for 
2014.10.28http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20141028/554bffae/attachment-0001.pdf).
  Before the rewrite the paths were a concatenation of the medication/NDF-RT 
names which got really long and messy.  I think you'll also find that the new 
code is much easier to read and better documented (hopefully).

For the newer code see 
epic_med_mapping.sqlhttps://informatics.kumc.edu/work/browser/heron_load/epic_med_mapping.sql
 on the KUMC Informatics wiki.  Or, update to a newer version of the KUMC ETL 
code from the GPC shared repository (see 
MultiSiteDevhttps://informatics.gpcnetwork.org/trac/Project/wiki/MultiSiteDev).
  The GPC tickets relevant to the medication mapping rewrite include 
#78https://informatics.gpcnetwork.org/trac/Project/ticket/78, 
#181https://informatics.gpcnetwork.org/trac/Project/ticket/181, and 
#152https://informatics.gpcnetwork.org/trac/Project/ticket/152.

Regards,

Nathan

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Munns, Michael B
Sent: Tuesday, December 02, 2014 3:59 PM
To: gpc-dev@listserv.kumc.edu
Subject: RxNorm metadata

I am working on the RxNorm metadata using the KU epic_med_mapping.sql script.

In there is the creation of a table rxnorm.clarity_name_to_rxcui_medex and then 
a second table is created off of that. I don't see where the
rxnorm.clarity_name_to_rxcui_medex gets populated from. There is a link a medex 
tool in the script. What am I missing?

Michael Munns
Database Analyst
402-559-3821


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Agenda for the gpc-dev call today from Jim McClay

[Nathan Graham]

All,

Here is the agenda for the call gpc-dev call today that Jim McClay sent out Tue 
11/4/2014 8:43 AM.  gpc-devhttp://listserv.kumc.edu/pipermail/gpc-dev/ wasn't 
in the copy list, but I think it's reasonably clear based on the e-mail 
discussion that he intended for it to be distributed to the group.

 1)Patient Generated Information according to PCORI
 2)Our proposal to PCORI dated 7-9-14
 3)Survey of network capabilities
 4)Next steps.

 Link to PCORI PRO Task Force Slides 
 https://pcornet.centraldesktop.com/taskforces/file/31721898/
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RE: GPC Terminology V1

[Nathan Graham]

Phillip,

Regarding the medication modifiers: The modifiers weren't showing up in the KU 
hierarchy because of an oversight/bug which I've addressed (er, manually fixed 
up) - see ticket 37 comment 
16https://informatics.gpcnetwork.org/trac/Project/ticket/37#comment:16.

As for GPC medications, there aren't any modifiers on Babel at this time.  I 
guess I didn't realize that we had decided on what medication modifiers we 
needed to support for GPC.   It looks like the CDM v2 draft has a dispensing 
table but I'm not sure it aligns with the KU modifier dispensed.  The CDM 
says outpatient pharmacy dispensing...not commonly captured within healthcare 
systems.  At KU, the dispensed modifier basically comes from the 
ORDER_DISP_INFO table Clarity Data Dictionary says: This table contains 
dispense information for orders but as I understood it, we (KU) don't have 
outpatient pharmacy information.  I thought we had a discussion about dispensed 
medications with respect to the CDM but I wasn't able to find record of it in 
the meeting notes from the past few weeks.  It's entirely possible I'm missing 
something right now.

I wonder if I should just include all the modifiers we have at KUMC?  Or does 
that add more complexity than we need/want?

Regards,

Nathan


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Tuesday, October 28, 2014 1:13 PM
To: Phillip Reeder
Cc: gpc-dev@listserv.kumc.edu
Subject: RE: GPC Terminology V1

Yes, it's good to get these details nailed down, Phillip.

The GPC standard for demographics has never been quite baked. We have never 
closed #67https://informatics.gpcnetwork.org/trac/Project/ticket/67. Yes, I 
hope we can converge on what Hubert uploads, and I hope he uploads it soon. I 
didn't negotiate a specific date with him, but I sure hope it's in the next few 
days.

I'm not sure what's up with modifiers on babel, but we've seen problems with 
that in the past. I heard Nathan say he made a note to look into it. I hope the 
problem is just on babel and if you download the CSV from the central desktop 
and deploy it locally, you'll get the modifiers.

Vitals in babel are labelled GPC: Clinical measurements. Your question 
suggests that's not very usable. Note that 
#23https://informatics.gpcnetwork.org/trac/Project/ticket/23 has been 
re-opened because Jim C. plans to (have Hubert) update some details of  the 
LOINC mapping.

Yes, the tumor registry should get the same treatment as the rest. Russ and 
Nathan and I have said yes, we should do that a few times; I just promoted it 
to a ticket: #185https://informatics.gpcnetwork.org/trac/Project/ticket/185.


--
Dan

From: Phillip Reeder [phillip.ree...@utsouthwestern.edu]
Sent: Tuesday, October 28, 2014 12:53 PM
To: Dan Connolly
Subject: GPC Terminology V1
Dan,
Based on today's call,  I want to make sure that I understand where we are on 
the 5 terminologies we are targeting for Milestone data-domains2.

Demographics - Are we using the PCORI Demographics, plus age in days?  I'm 
not clear on what the GPC standard is but maybe when Hubert uploads his piece 
to babel it will be more clear.  Is there a date for this?
Diagnosis - ICD9 Hierarchy built in babel,  Approved.
Medications - Medication Hierarchy built in babel.  I think the modifiers still 
need to be added to this hierarchy.
Vitals - Is there a proposed GPC vital signs terminology?  I'm not seeing it in 
Babel.
Tumor Registry - We are all using the same KU code so we should, in theory, 
have the same paths/codes.  But since the terminology is generated from the 
data, is there a chance we won't see all possible values from a given site?  
Can someone produce a GPC Tumor Registry terminology as the standard and put it 
on Babel as GPC:Tumor Registry?  Or as an interim way to show it, maybe just 
duplicate KUMC's terminology and put GPC before it so we see that it's there.

Does my understanding seem correct as to where we are?

Thanks,
Phillip

Feel free to reply to the group, or just to me if I'm way off:).






UT Southwestern Medical Center
The future of medicine, today.
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RE: gpc-dev agenda 21 Oct

[Nathan Graham]

WISC is having technical issues - here's a google 
dochttps://docs.google.com/document/d/19VwtMX3n7EPLmWcG0_X_T5LfQJ3ycz1B13MUJnh0Io0/edit?usp=sharing
 for notes.

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Verhagen, Laurel A
Sent: Monday, October 20, 2014 2:56 PM
To: gpc-dev@listserv.kumc.edu
Subject: RE: gpc-dev agenda 21 Oct

Hi all,

Revised agenda below.

Thanks,
Laurel

From: 
gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Verhagen, Laurel A
Sent: Monday, October 20, 2014 1:10 PM
To: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: gpc-dev agenda 21 Oct

Let me know if you have anything to add or change. Agenda for 10/21/2014:


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

a.   Meeting ID and access code: 
686-845-717https://global.gotomeeting.com/meeting/join/686845717; call +1 
(267) 507-0008

b.  Meeting notes 
(#12https://informatics.gpcnetwork.org/trac/Project/ticket/12): 14 Oct notes 
(attached) OK?  today's scribe:  WISC

c.   Roll: all 10 DevTeams represented? Comments on the agenda?

   i.  KUMC, 
CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW

d.  new/closed/reopened tickets:

   i.  
#152https://informatics.gpcnetwork.org/trac/Project/ticket/152 AUI-based med 
ontology (complete)

 ii.  
#163https://informatics.gpcnetwork.org/trac/Project/ticket/163 PMN at UNMC 
(complete)

iii.  
#86https://informatics.gpcnetwork.org/trac/Project/ticket/86 Verify ONC 
Guidelines for demographic/patient observables (dup)

e.  Next meeting: 28 Oct. Scribe volunteer?

f.Reminder for Nov 4: Informatics Leads expected to join Jim McClay, 
Russ, Betsy C. to discuss Implementation of patient generated information 
approach (PMO milestone 4.19, 
#102https://informatics.gpcnetwork.org/trac/Project/ticket/102)

2.   #176https://informatics.gpcnetwork.org/trac/Project/ticket/176: 
Implement data validation and quality approaches - due this month

a.   #178https://informatics.gpcnetwork.org/trac/Project/ticket/178 - 
need definition to complete PMO milestone2.6

b.  Run base set of quality queries built for 
#70https://informatics.gpcnetwork.org/trac/Project/ticket/70

c.   Report results to Tom Mish

3.   DSSNI Updates - first query distributed winter 2014/2015? Other 
updates?

4.   PCORnet CDM v2.0 Draft - volunteers to review and comment; feedback 
due 10/29

5.   Alignment on Medications 
(#160https://informatics.gpcnetwork.org/trac/Project/ticket/160, 
#78https://informatics.gpcnetwork.org/trac/Project/ticket/78) - anything new?

6.   Empirical Data Dictionary Alex Bokov (re 
#132https://informatics.gpcnetwork.org/trac/Project/ticket/132, 
#106https://informatics.gpcnetwork.org/trac/Project/ticket/106) - anything 
new?

7.   Encryption of data at rest (stipulation of the GPC Agreement) - how 
are sites handing this?

8.   #31https://informatics.gpcnetwork.org/trac/Project/ticket/31: data 
elements for ALS cohort characterization - this was on the agenda last time. 
Still needed?

9.   Non-agenda topics

Thanks,
Laurel


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Towards determining how Catchment Area is defined at KU

[Nathan Graham]

All,

As per the GPC-Dev September 2 meeting 
noteshttp://listserv.kumc.edu/pipermail/gpc-dev/attachments/20140902/c96d8ee6/attachment-0001.pdf,
 I e-mailed my contacts on the KU hospital Organizational Improvement/Reporting 
teams last Wednesday in an effort to find out how KU defines catchment area.  
I'll e-mail gpc-dev with what I learn.  I'm also interested to see what other 
GPC sites find out.

Thanks.

Regards,

Nathan
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KUMC Drafts: ETL Data Dictionary (#144) and CDM Compliance (#114)

[Nathan Graham]

Dr. Campbell/All,

I've uploaded a draft of the ETL Annotated Data Dictionary for 
KUMChttps://pcornet.centraldesktop.com/c4gpc/file/33713907/ (see GPC ticket 
144 comment 
17https://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:17) and 
a draft of the PCORI CDM Compliance Worksheet for 
KUMChttps://pcornet.centraldesktop.com/c4gpc/file/33714066/ (see GPC ticket 
114 comment 
25https://informatics.gpcnetwork.org/trac/Project/ticket/114#comment:25) to 
the PCORNet Central Desktop.  I don't know whether these are the drafts that 
will be submitted to PCORI or not - I guess it depends on what's found if/when 
they're reviewed.

See the 
pcori-annotated-data-dictionaryhttps://bitbucket.org/njgraham/pcori-annotated-data-dictionary
 on BitBucket project for details on how the numbers in the worksheets were 
derived.  Most relevant:

-  
CDM_transform.sqlhttps://bitbucket.org/njgraham/pcori-annotated-data-dictionary/src/b95623392a1fca8741ae388a9ac4b3e86ff7150e/CDM_transform.sql?at=default
 along with 
heron_to_pcori.csvhttps://bitbucket.org/njgraham/pcori-annotated-data-dictionary/src/b95623392a1fca8741ae388a9ac4b3e86ff7150e/heron_to_pcori.csv?at=default
 is what I used to build the CDM tables by mapping HERON i2b2 paths to the 
PCORI i2b2 paths that Dan builthttps://bitbucket.org/DanC/pcornet-dm.

-  
ETL_dict_queries.sqlhttps://bitbucket.org/njgraham/pcori-annotated-data-dictionary/src/b95623392a1fca8741ae388a9ac4b3e86ff7150e/ETL_dict_queries.sql?at=default
 is what I used to fill in the spreadsheet numbers based on the CDM tables.

I welcome comments/suggestions.

I wonder if you (Dr. Campbell) should own the ETL Annotated Data Dictionary 
form required by 
PCORIhttps://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:17 
ticket?  As I understand it, you are collecting the spreadsheets to submit to 
PCORI, right?  Note that I made a folder on the PCORNet Central 
Desktophttps://pcornet.centraldesktop.com/c4gpc/folder/4142694/#folder:4134009
 for sites to put their data dictionary spreadsheets.

--
Nathan

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RE: gpc-dev agenda 29 July

[Nathan Graham]

Google 
docshttps://docs.google.com/document/d/1nbpkvmizdpTEH2I-p8c1RPbEmOEawc33DpvVoZD8lSA/edit?usp=sharing
 for notes.

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Tuesday, July 29, 2014 10:32 AM
To: gpc-dev@listserv.kumc.edu
Subject: RE: gpc-dev agenda 29 July



  1.  Convene, take roll, review records and plan next meeting
 *   ​Meeting ID and access code: 
686-845-717https://global.gotomeeting.com/meeting/join/686845717; call +1 
(267) 507-0008
 *   meeting notes 
(#12https://informatics.gpcnetwork.org/trac/Project/ticket/12): previous 
notes OK? today's scribe Wisconsin
 *   roll: all 10 
DevTeamshttps://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams 
represented? comments on the agenda?
KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW
*   new/closed/reopened tickets - see 
#93https://informatics.gpcnetwork.org/trac/Project/ticket/93 babel site below
*   impact of JRC's ... Problem (IT) Terminology 2014 R2.3 Update ... 
message not clear to me; add it to the agenda?
 *   next meeting: 5 Aug. scribe volunteer?
  2.  #67https://informatics.gpcnetwork.org/trac/Project/ticket/67 
demographics (age) and mapping to CDM 
(#114https://informatics.gpcnetwork.org/trac/Project/ticket/114, 
#144https://informatics.gpcnetwork.org/trac/Project/ticket/144 ?)
 *   ​PCORI 
Mappinghttp://listserv.kumc.edu/pipermail/gpc-dev/2014q3/000311.html from 
Reeder and others
 *   pcori_cdm_pitt_etl_scripts.zip
  3.  #144https://informatics.gpcnetwork.org/trac/Project/ticket/144 Extract, 
Transform, and Load (ETL) Annotated Data Dictionary
 *   IOWA designee?
  4.  
DataSharinghttps://informatics.gpcnetwork.org/trac/Project/wiki/DataSharing: 
#14https://informatics.gpcnetwork.org/trac/Project/ticket/14 
PopMedNet?https://informatics.gpcnetwork.org/trac/Project/wiki/PopMedNet, 
#143https://informatics.gpcnetwork.org/trac/Project/ticket/143 sample query
 *   looks more likely that each site will have to have their whole i2b2 
repository available in CDM format 
(#145https://informatics.gpcnetwork.org/trac/Project/ticket/145) which means 
our federated 
DataSharinghttps://informatics.gpcnetwork.org/trac/Project/wiki/DataSharing 
design won't work for PCORNet 
PopMedNet?https://informatics.gpcnetwork.org/trac/Project/wiki/PopMedNet 
queries; each site will likely need their own 
PopMedNet?https://informatics.gpcnetwork.org/trac/Project/wiki/PopMedNet node.
 *   First PCORnet Test Query Completed!, says PCORnet Weekly 
Announcement - July 28, 2014.
 *   MCRF's node is up; which site to go next?
*   declare victory on 
#14https://informatics.gpcnetwork.org/trac/Project/ticket/14, or just 
re-scope it and reassign it to the next site?
*   Try test query at MCRF?
  5.  #31https://informatics.gpcnetwork.org/trac/Project/ticket/31 data 
elements for ALS cohort characterization
 *   discussion in July 25 ALS call 
(ticket:31#comment:14https://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:14)
 was tabled
 *   Wendy sent a proposal for follow-up to Russ
  6.  #139https://informatics.gpcnetwork.org/trac/Project/ticket/139 
insurance status
 *   Justin, any news?
  7.  babel site design 
#123https://informatics.gpcnetwork.org/trac/Project/ticket/123, account tools 
#93https://informatics.gpcnetwork.org/trac/Project/ticket/93
 *   
milestone:heron-workshop2https://informatics.gpcnetwork.org/trac/Project/milestone/heron-workshop2
  8.  #56https://informatics.gpcnetwork.org/trac/Project/ticket/56: shareable 
synthetic test data sets and 
ModelMashUphttps://informatics.gpcnetwork.org/trac/Project/wiki/ModelMashUp
 *   FYI: Jeff Brown is looking into sharing a 50K patient mini-sentinel 
data set. Next checkpoint: 12pm call (immediately following gpc-dev)

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RE: gpc-dev 10 June agenda: what's up at your site?

[Nathan Graham]

I plan to scribe this time.  I've started a Google 
Documenthttps://docs.google.com/document/d/1lYPH_1Blb0hye8TgmGln482SfCGZ-XWtc6WWH15XfiA/edit
 we can use - editable by anyone with the link.

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, June 09, 2014 2:33 PM
To: gpc-dev@listserv.kumc.edu
Subject: RE: gpc-dev 10 June agenda: what's up at your site?

What are the main (informatics related) things going on at your site?

Bonus points for letting everybody know by email before tomorrow's call.

Otherwise, we'll talk about it then.

The work by site 
listhttps://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams#WorkBySite 
is getting a little stale; here's hoping we can update it.

--
Dan

From: Dan Connolly
Sent: Monday, June 09, 2014 12:16 PM
To: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: gpc-dev 10 June agenda: in progress
I'm running a bit behind today; stay tuned...


--
Dan
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You can now modify the CC field on GPC wiki tickets.

[Nathan Graham]

Dr. Campbell,

As you noted, you couldn’t previously change the CC field in a ticket on the 
GPC Wiki 
sitehttps://informatics.gpcnetwork.org/trac/Project/admin/general/perm.  Now, 
it should be such that anyone who can log in can also modify the CC.

Thanks.

Regards,

Nathan

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Feedback on GPC ticket 114 (Milestone 2.7)

[Nathan Graham]

Dr. Campbell,

I took a look at the queries - here are the main points I noticed.  Dan or Russ 
may have further comments.  The actual SQL I ran against our database (based on 
your queries in GPC ticket 
114https://informatics.gpcnetwork.org/trac/Project/ticket/114) is attached.

* Ethnicity_cd isn't part of the patient dimension

* Facility_location isn't part of the visit dimension, but perhaps the 
location_cd (linking to the code_lookup table) gets what we need (see CRC 
Design 
Documenthttps://www.i2b2.org/software/files/PDF/current/CRC_Design.pdf).   At 
KU, we don't fill in the provider dimension.

* Encountertype_cd isn't part of the visit dimension and I don't see 
anything that I think might be analogous.

* At KU, we don't have any LOINC concepts loaded to my knowledge, but I 
think we have most of the concepts  you mentioned in our flowsheet category 
(height, weight, bp, etc).  We also have discharge disposition as facts (rather 
than modifiers).  We do have modifiers for some billing types (clinic, 
hospital, and primary diagnosis).
Minor points:

* I2b2 calls it the visit_dimension now, not encounter_dimension

* A few column names are different - I noted them in the attached SQL.

Thanks.

Regards,

Nathan



GPC_114.sql
Description: GPC_114.sql
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Re: cohort characterization data elements scavenger hunt in babel

[Nathan Graham]

All,

One workaround for the 3 minute query timeout that Dan mentioned is to change 
the default timeout from 180 seconds to 1 second after logging in to the 
webclient.

To do this, select the icon with a green check mark in the top right of the 
query tool tab in the webclient.  Then, set timeout to 1 second.  The 
webclient will still report that the query timed out but it will do so very 
quickly after running the query rather than 3 minutes later.

See ticket #24 comment 
4http://informatics.gpcnetwork.org/trac/Project/ticket/24?cnum_edit=4#comment:4
 for screenshots.

I plan to keep looking for the root of the problem that causes the queries to 
time out (rather than returning a count of 0 patients right away like I think 
it should).  But, the workaround noted above would likely save time for those 
working on the scavenger hunt.

Thanks.

Regards,

Nathan

From: Greater Plains Collaborative Software Development 
[mailto:GPC-DEV@LISTSERV.KUMC.EDU] On Behalf Of Dan Connolly
Sent: Monday, February 03, 2014 1:03 AM
To: GPC-DEV@LISTSERV.KUMC.EDU
Subject: cohort characterization data elements scavenger hunt in babel

Now that 
babelhttp://informatics.gpcnetwork.org/trac/Project/wiki/SoftwareDev#babel is 
more or less working, in discussion with Russ and Jim, we did this exercise a 
couple times of picking a proposed data element for characterizing our ALS, 
breast cancer, or obesity cohort from table 6.1 of the GPC 
proposalhttp://frontiersresearch.org/frontiers/sites/default/files/frontiers/documents/GPC-PCORI-CDRN-Research-Plan-Template-KUMCv44.pdf
 and looking it up in the terminologies from each of our sites:



The data elements save test shows that it's possible to save a query and 
hence a set of terms, even though there are no facts in the system. 
Unfortunately, it's a bit tedious due to...

  *   #24http://informatics.gpcnetwork.org/trac/Project/ticket/24 babel 
queries run 3 minutes before they're available for saving, sharing
But you can see that we found some BCRA1 cancer marker terms. And I was a 
little puzzled by what I found for BMI, just within my own back yard (KUMC 
HERON).

As I thought about doing this for even a dozen or so data elements for each 
cohort across our sites, I realize this is a lot of work. So after a few more 
kinks are worked out, I'm inclined to start a sort of scavenger hunt to 
crowdsource the work:

  *   1 point for saving a query of any sort in the SHARED folder. (like the 
data elements save test)

 *   up to 3 per team. No grinding. ;-)

  *   5 points for a query that shows use of one of the proposed data elements 
from at least one site, clearly indicating the relevant cohort(s). (BCRA1 would 
qualify, if I put breast cancer in the name (or put it in a breast cancer 
subfolder of SHARED, which doesn't work just yet))
  *   10 points for a query that shows consistent use of such an i2b2 concept 
across at least two sites.
  *   15 points for a query that turns up a data modelling issue based on 
differences in i2b2 usage within or between sites (like the BMI query that 
turned into #23http://informatics.gpcnetwork.org/trac/Project/ticket/23)
  *   30 points for a query that captures the results of surveying all the 
sites for some data element
  *   add 15 points to the above for coordinating with the relevant cohort 
experts to get them to endorse the usage as sensible.
  *   40 points for taking something from table 6.1 that's too vague, such as 
diagnostic tests and coordinating with the relevant ALS/cancer/obesity 
experts to refine it to one or more terms that we might expect to find in our 
i2b2 data
  *   100 points for a query that is endorsed by the respective cohort experts 
as capturing all of the data elements necessary to do (preliminary) cohort 
characterization.
Multipliers for use of MU2 standards should fit in there somewhere... hmm...

While we're working the kinks out, I'm open to input on what the points should 
be redeemable for. ;-)

--
Dan