date:20170320

gpc-dev 21 Mar agenda and meeting notes

2017-03-20 Thread Dan Connolly

What else for tomorrow?

  *   21 Mar gpc-dev shared 
notes
 scribe: MU




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

 *   11:00am Central Time.
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: MU

 *   comments on the agenda? On last week’s notes? 
(#12)
Recent tickets 
opened/closed - FYI 
(i.e. not intended for discussion)

*   none

 *   Next Meetings:
Note LRU scribe schedule in 
#12

*   28 Mar: Dan at AMIA. Cancel? Recruit chair?

*   4 Apr scribe: UTHSCSA?

*   Integrating hospital billing: UHC ETL 
scripts - 
preferred date to discuss?

  2.  
Milestone:grouse-research-1

 *   #564 (Crosswalk files from 6 sites back from GDIT) 
closed 
fixed!
Overlap between CMS data and KUMC finder file: ~1.4M

  3.  
Milestone:cdm-cycle3
 checkpoint ~3 Apr

 *   #580 Data 
Characterization - Cycle 2, Refresh 2 
Tracking:
Here's a list of themes received by one or more sites:

1


Incorrect CDM version in HARVEST table. Update to 3.0.


WISC


2


Incorrect DATAMART_NAME in HARVEST table.


Marshfield, Regenstrief Indiana, KUMC, UTHSCSA


3


the % of encounters without a principal diagnosis was calculated incorrectly in 
the EDC report/will be below 10% threshold.


Marshfield, UNMC, Regenstrief Indiana, UTHSCSA


4


Future Dates - enrollment end date (July 2016) after refresh date (June 2016)


Iowa


5


ICD9 diagnosis codes do not appear to be valid codes


KUMC


6


ICD10 diagnosis codes do not appear to be valid codes


Regenstrief/Indiana?,
 UTHSCSA (100%), Either Missouri or Minnesota (message sent to T.Meyer, but 
datamart referenced was C4UMO not C4UMA)


7


Data coded as ICD9 after the ICD9/10 transition dates in the Diagnosis and 
Procedures tables.


Iowa


8


Orphan Encounter IDs - if the encounter appears on a data record, it's expected 
to exist in the Encounter table


Iowa


9


Dispensing records in DataMart_All, but nothing in Dispensing DC


Iowa



 *   CDM V3.X PROCEDURES
JRC: during 
DRNOC discussions, it became clear that how the procedures tables is populated 
varies widely between datamarts - 12x in some cases.
Labs were deemed relevant to be coded as procedures.  What is appropriate for 
GPC to fall under the procedure tables?
Discussion continued after the scheduled time; it wasn’t entirely conclusive.

 *   interoperable procedure order ontology by looking at link between 
orders and billing 
transactions?  
Russ Waitman

  1.  
Milestone:snow-shrine-1
 due 20 Mar

 *   #460 SNOW 
SHRINE node at UTSW
SNOW Shrine 
Ontologies   
Phillip Reeder Thu Mar 9

 *   Update shrine-1 milestone ETA? I.e. leading sites (WISC, UTSW, MCRF, 
IU) operational

  2.  
Milestone:snow-shrine-2
 due ~Apr

 *   #280, 
MEDICATIONS metadata for SCILHS

*   UNMC will install SCILHS metadata into Babel.

*   Note Russ/KUMC March 15 feedback 
comment:16

*   JRC to solicit input Marsolo and company from the national 
antibiotics study
https://github.com/CDMFORUM/CDM-GUIDANCE/issues

*   Tom/Debbie/WISC 
review

 *   Status at shrine-2 sites:

*   KUMC 
#567: we’re m

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

2017-03-20 Thread Debbie Yoshihara

Ok, here is how I count 11

1) RX_BASIS DI
2) RX_BASIS PR
3) RX_BASIS AD
4) RX_DAYS_SUPPLY
5) RX_FREQ
6) RX_QUANTITY
7) RX_REFILLS
8) RX_STRENGTH
9) RX_ROUTE
10) RX_DOSE
11) RX_DETAIL

I guess you're counting the RX_BASIS as 1 instead of 3.

--- Debbie Yoshihara

-Original Message-
From: Dan Connolly [mailto:dconno...@kumc.edu] 
Sent: Monday, March 20, 2017 10:38 AM
To: Debbie Yoshihara; gpc-dev@listserv.kumc.edu; Thomas Mish; 
campb...@unmc.edu; huhick...@nebraskamed.com; Russ Waitman
Cc: jeff.kl...@mgh.harvard.edu
Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

As to who is going to look at them: i2p-transform (i.e. software to build 
PCORNet CDM from i2b2) consumes these modifiers.

As to 11x: how many modifiers are you currently storing? You're already storing 
RX_BASIS, RX_FREQUENCY, RX_DAYS_SUPPLY, RX_QUANTITY, and RX_REFILLS somehow, 
yes?

UNMC was proposing adding RX_STRENGTH, RX_ROUSE, RX_DOSE, and RX_SIG, but in 
discussion it emerged that "justification for including route, dose and detail 
modifiers ... is weakest in terms of use cases"

I count 9 total modifiers in the proposal, 5 of which KUMC (and presumably the 
other 8 sites using the i2p-transform code) are already loading, and 3 of which 
could (from discussion so far) be removed without much objection. So to me, it 
looks like this is a proposal to go from 5 to 6 modifiers.

-- 
Dan


From: Debbie Yoshihara [dlyos...@wisc.edu]
Sent: Monday, March 20, 2017 10:09 AM
To: gpc-dev@listserv.kumc.edu; Thomas Mish; campb...@unmc.edu; 
huhick...@nebraskamed.com; Dan Connolly; Russ Waitman
Cc: jeff.kl...@mgh.harvard.edu
Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

I have looked over these explosion of modifiers.
For the med modifiers if you populated all of them that would make the facts 
11x bigger for the med facts.
Who is going to look at all of these? Or even populate them if they have them?

The only other question I have is for the lab_mod, what is the difference 
between stat and expedite?

--- Debbie Yoshihara



-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC 
Informatics
Sent: Monday, March 20, 2017 8:46 AM
To: Thomas Mish; campb...@unmc.edu; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

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

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

2017-03-20 Thread Phillip Reeder

The explosion of the number of facts has been my biggest concern with the
med modifiers as well.  With 115 million medication rows, a 10x increase
would give us double our existing number of facts. At UTSW, I¹ve populated
the data for many of these modifiers into the observation_blob column in a
flat XML schema. This allows me to use them in my ETL for the PCORI CDM.
But it doesn¹t allow me to query on them in i2b2. It would be nice if i2b2
could be modified to allow me use that XML data in a query, but for now,
it¹s meeting my needs.  However with the SHRINE work we are doing, I might
be forced to populate them as modifiers.


Phillip

On 3/20/17, 10:37 AM, "Gpc-dev on behalf of Dan Connolly"
 wrote:

>As to who is going to look at them: i2p-transform (i.e. software to build
>PCORNet CDM from i2b2) consumes these modifiers.
>
>As to 11x: how many modifiers are you currently storing? You're already
>storing RX_BASIS, RX_FREQUENCY, RX_DAYS_SUPPLY, RX_QUANTITY, and
>RX_REFILLS somehow, yes?
>
>UNMC was proposing adding RX_STRENGTH, RX_ROUSE, RX_DOSE, and RX_SIG, but
>in discussion it emerged that "justification for including route, dose
>and detail modifiers ... is weakest in terms of use cases"
>
>I count 9 total modifiers in the proposal, 5 of which KUMC (and
>presumably the other 8 sites using the i2p-transform code) are already
>loading, and 3 of which could (from discussion so far) be removed without
>much objection. So to me, it looks like this is a proposal to go from 5
>to 6 modifiers.
>
>--
>Dan
>
>
>From: Debbie Yoshihara [dlyos...@wisc.edu]
>Sent: Monday, March 20, 2017 10:09 AM
>To: gpc-dev@listserv.kumc.edu; Thomas Mish; campb...@unmc.edu;
>huhick...@nebraskamed.com; Dan Connolly; Russ Waitman
>Cc: jeff.kl...@mgh.harvard.edu
>Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by
>ingredient
>
>I have looked over these explosion of modifiers.
>For the med modifiers if you populated all of them that would make the
>facts 11x bigger for the med facts.
>Who is going to look at all of these? Or even populate them if they have
>them?
>
>The only other question I have is for the lab_mod, what is the difference
>between stat and expedite?
>
>--- Debbie Yoshihara
>
>
>
>-Original Message-
>From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC
>Informatics
>Sent: Monday, March 20, 2017 8:46 AM
>To: Thomas Mish; campb...@unmc.edu; huhick...@nebraskamed.com;
>dconno...@kumc.edu; rwait...@kumc.edu
>Cc: gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
>Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by
>ingredient
>
>#280: Medication ontology orgainzed by ingredient
>-+
> Reporter:  preeder  |   Owner:  mish
> Type:  enhancement  |  Status:  assigned
> Priority:  major|   Milestone:  snow-shrine-2
>Component:  data-stds|  Resolution:
> Keywords:   |  Blocked By:
> Blocking:   |
>-+
>Changes (by dconnolly):
>
> * owner:  jay.pedersen => mish
>
>
>Comment:
>
> Tom,
>
> Is Debbie likely to complete her review this morning?
>
>--
>Ticket URL:
>
>gpc-informatics 
>Greater Plains Network - Informatics
>___
>Gpc-dev mailing list
>Gpc-dev@listserv.kumc.edu
>http://listserv.kumc.edu/mailman/listinfo/gpc-dev
>___
>Gpc-dev mailing list
>Gpc-dev@listserv.kumc.edu
>http://listserv.kumc.edu/mailman/listinfo/gpc-dev




UT Southwestern


Medical Center



The future of medicine, today.


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

2017-03-20 Thread Dan Connolly

As to who is going to look at them: i2p-transform (i.e. software to build 
PCORNet CDM from i2b2) consumes these modifiers.

As to 11x: how many modifiers are you currently storing? You're already storing 
RX_BASIS, RX_FREQUENCY, RX_DAYS_SUPPLY, RX_QUANTITY, and RX_REFILLS somehow, 
yes?

UNMC was proposing adding RX_STRENGTH, RX_ROUSE, RX_DOSE, and RX_SIG, but in 
discussion it emerged that "justification for including route, dose and detail 
modifiers ... is weakest in terms of use cases"

I count 9 total modifiers in the proposal, 5 of which KUMC (and presumably the 
other 8 sites using the i2p-transform code) are already loading, and 3 of which 
could (from discussion so far) be removed without much objection. So to me, it 
looks like this is a proposal to go from 5 to 6 modifiers.

-- 
Dan


From: Debbie Yoshihara [dlyos...@wisc.edu]
Sent: Monday, March 20, 2017 10:09 AM
To: gpc-dev@listserv.kumc.edu; Thomas Mish; campb...@unmc.edu; 
huhick...@nebraskamed.com; Dan Connolly; Russ Waitman
Cc: jeff.kl...@mgh.harvard.edu
Subject: RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

I have looked over these explosion of modifiers.
For the med modifiers if you populated all of them that would make the facts 
11x bigger for the med facts.
Who is going to look at all of these? Or even populate them if they have them?

The only other question I have is for the lab_mod, what is the difference 
between stat and expedite?

--- Debbie Yoshihara



-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC 
Informatics
Sent: Monday, March 20, 2017 8:46 AM
To: Thomas Mish; campb...@unmc.edu; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

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

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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RE: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

2017-03-20 Thread Debbie Yoshihara

I have looked over these explosion of modifiers.
For the med modifiers if you populated all of them that would make the facts 
11x bigger for the med facts.
Who is going to look at all of these? Or even populate them if they have them?

The only other question I have is for the lab_mod, what is the difference 
between stat and expedite?

--- Debbie Yoshihara



-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC 
Informatics
Sent: Monday, March 20, 2017 8:46 AM
To: Thomas Mish; campb...@unmc.edu; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

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

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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Re: [gpc-informatics] #580: Data Characterization - Cycle 2, Refresh 2 Tracking

2017-03-20 Thread GPC Informatics

#580: Data Characterization - Cycle 2, Refresh 2 Tracking
---+-
 Reporter:  lv |   Owner:  nsmith
 Type:  problem|  Status:  assigned
 Priority:  major  |   Milestone:  cdm-cycle3
Component:  data-stds  |  Resolution:
 Keywords:  CDM, DCQ, EDC  |  Blocked By:
 Blocking: |
---+-
Changes (by dconnolly):

 * owner:  mprittie => nsmith


Comment:

 Nick and everybody,

 Note Laurel elaborated comment:1 to clarify which issues apply to which
 sites. UIOWA is the winner with 4 issues. Please let us know your plan to
 address them.

 UIOWA is not alone; the full list of sites with issues identified is:
 UIOWA, WISC, MCRF, IU, KUMC, UTHSCSA, UNMC, and either MU or UMN. I'd like
 a plan for each of those sites, please.

 For anything where we don't have a straightforward plan identified, I may
 find it useful to make a separate ticket.

--
Ticket URL: 

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

2017-03-20 Thread Thomas Mish

I don't think so. 

-TM

-Original Message-
From: GPC Informatics [mailto:d...@madmode.com] 
Sent: Monday, March 20, 2017 8:46 AM
To: Thomas Mish ; campb...@unmc.edu; huhick...@nebraskamed.com; 
dconno...@kumc.edu; rwait...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu; mprit...@kumc.edu; jeff.kl...@mgh.harvard.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

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

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
___
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu
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Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

2017-03-20 Thread GPC Informatics

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

 * owner:  jay.pedersen => mish


Comment:

 Tom,

 Is Debbie likely to complete her review this morning?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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gpc-dev 21 Mar agenda and meeting notes

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

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

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

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

Re: [gpc-informatics] #580: Data Characterization - Cycle 2, Refresh 2 Tracking

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

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

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