Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+---
 Reporter:  campbell |   Owner:  campbell
 Type:  task |  Status:  closed
 Priority:  major|   Milestone:  initial-data-domains
Component:  data-stds|  Resolution:  fixed
 Keywords:  ETL Data Dictionary  |  Blocked By:
 Blocking:   |
-+---
Changes (by campbell):

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


Comment:

 PCORI accepted our ETL ADDS
 Singing off
 Jim

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+---
 Reporter:  campbell |   Owner:  campbell
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  initial-data-domains
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:
 Blocking:   |
-+---
Changes (by dconnolly):

 * blockedby:  145, 146 =>


Comment:

 I think there are a few details left in #145 and #146, but they're no
 longer blocking this work.

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+---
 Reporter:  campbell |   Owner:  campbell
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  initial-data-domains
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+---

Comment (by nateapathy):

 I've uploaded my draft of the
 [https://pcornet.centraldesktop.com/c4gpc/file/33770797/ CMH ETL Annotated
 Data Dictionary] to the PCORNet Central Desktop

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+---
 Reporter:  campbell |   Owner:  campbell
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  initial-data-domains
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+---

Comment (by campbell):

 At the DSSNI call last week Jeff Brown clarified that there was no
 algorithm that PCORI had for enrollment and the point was to get an
 estimate of the denominator of patients for study design.He urged
 everyone to choose what best suits their organization geopolitically and
 ethnographically.  Recognizing that none of us, except perhaps Marshfield,
 has closed panels where we provide all care, I suggest that each GPC site
 choose one or more of the strategies below and we will compare our stats
 to see if we want to preferentially require an approach for GPC the
 network:

 Geography: all patients within 50 miles of the site
 Algorithmic: all 12 month periods when the patient had two separate face-
 to-face encounters (IP, ED or AV) at the institution OR a single visit
 billed for wellness care
 Encounters: period of time from the first til the last face-to-face
 encounter (IP, ED, AV)
 Insurance: period of an active policy duration for any prime vendor (HMO-
 type) insurance contracts with the organization

 Jim

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+---
 Reporter:  campbell |   Owner:  campbell
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  initial-data-domains
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+---

Comment (by campbell):

 UNMC draft ETLADD uploaded to PCORI desktop...thanks for the inspiration,
 Glen!

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+---
 Reporter:  campbell |   Owner:  campbell
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  initial-data-domains
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+---

Comment (by gbushee):

 Uploaded MCW draft of Annotated Data Dictionary with numbers to:

 https://pcornet.centraldesktop.com/c4gpc/folder/4134009/#folder:4134009

 - Glenn

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Campbell, James R]

I was Nathan but as I understand the minutes of this weeks call, the plan 
changed to uploading to PCORI desktop?  I am fine with that and we we will 
track our 10 site reports there with review on Tuesday
Jim

James R. Campbell MD
campb...@unmc.edu
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230

> On Aug 28, 2014, at 4:53 PM, "GPC Informatics"  wrote:
>
> #144: ETL Annotated Data Dictionary form required by PCORI
> -+---
> Reporter:  campbell |   Owner:  campbell
> Type:  task |  Status:  assigned
> Priority:  major|   Milestone:  initial-data-domains
> Component:  data-stds|  Resolution:
> Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
> Blocking:   |
> -+---
> Changes (by ngraham):
>
> * owner:  ngraham => campbell
>
>
> Comment:
>
> Dr. Campbell,
>
>> [http://listserv.kumc.edu/pipermail/gpc-dev/2014q3/000430.html As I
> understand it, you are collecting the spreadsheets to submit to PCORI,
> right?]
>
> I'll reassign to you...though that makes you the reporter (customer) and
> the owner which might not be ideal.
>
> --
> Ticket URL: 
> 
> gpc-informatics 
> Greater Plains Network - Informatics

The information in this e-mail may be privileged and confidential, intended 
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+---
 Reporter:  campbell |   Owner:  campbell
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  initial-data-domains
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+---
Changes (by ngraham):

 * owner:  ngraham => campbell


Comment:

 Dr. Campbell,

 >[http://listserv.kumc.edu/pipermail/gpc-dev/2014q3/000430.html As I
 understand it, you are collecting the spreadsheets to submit to PCORI,
 right?]

 I'll reassign to you...though that makes you the reporter (customer) and
 the owner which might not be ideal.

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+---
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  initial-data-domains
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+---

Comment (by ngraham):

 I've uploaded a draft of the
 [https://pcornet.centraldesktop.com/c4gpc/file/33713907/ ETL Annotated
 Data Dictionary for KUMC] to the PCORNet central desktop.

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Supreet Kathpalia]

Thanks for your response on the encounter type of the ETL-ADD.

At UMN we also plan to use a combination of DISP_ENC_TYPE and ADT_PAT_CLASS
to determine each of the encounter types for the PCORI  CDM.

Thanks,
Supreet




On Tue, Aug 26, 2014 at 11:41 AM, GPC Informatics  wrote:

> #144: ETL Annotated Data Dictionary form required by PCORI
> -+---
>  Reporter:  campbell |   Owner:  ngraham
>  Type:  task |  Status:  assigned
>  Priority:  major|   Milestone:  initial-data-domains
> Component:  data-stds|  Resolution:
>  Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
>  Blocking:   |
> -+---
>
> Comment (by ngraham):
>
>  I created a
>  [https://pcornet.centraldesktop.com/c4gpc/folder/4134009/#folder:4134009
>  folder on the PCORnet Central Desktop] for us to share our ETL data
>  dictionaries as suggested the gpc-dev call on 2014.08.26.
>
> --
> Ticket URL: <
> http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:16>
> gpc-informatics 
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-- 
Regards,
Supreet Kathpalia
Clinical Data Analyst
Research Development & Support
AHC Information Systems, U of MN
Ph. 612.624.5848
budh0...@umn.edu
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+---
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  initial-data-domains
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+---

Comment (by ngraham):

 I created a
 [https://pcornet.centraldesktop.com/c4gpc/folder/4134009/#folder:4134009
 folder on the PCORnet Central Desktop] for us to share our ETL data
 dictionaries as suggested the gpc-dev call on 2014.08.26.

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+---
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  initial-data-domains
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+---
Changes (by dconnolly):

 * milestone:  popmednet => initial-data-domains


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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by ngraham):

 I believe I've made enough progress on the [https://bitbucket.org/njgraham
 /pcori-annotated-data-dictionary/src pcori-annotated-data-dictionary] to
 answer the data summary questions tab in the spreadsheet.

 I wrote a bit of Python to run the queries (against our Oracle i2b2
 tables) and fill in the spreadsheet automatically.  Unfortunately,
 [http://www.python-excel.org/ Python Excel] module I'm using doesn't
 support editing in place or writing out fancy formatting in .xlsx files.
 Oh well, it was fun to write and at least it does output the relevant
 numbers in the right places in an un-formatted copy of the spreadsheet.
 See [https://bitbucket.org/njgraham/pcori-annotated-data-
 dictionary/src/a1b4dc404358fae52e4ceffcbd2646027880fec5/README.rst?at=default
 README.rst] for details.

 As for the PCORnet ETL Annotated Data Dictionary spreadsheet, I plan to
 finish up the textual descriptions and attach (or upload to the PCORNet
 Central Desktop) a draft for KU within the next couple of days.

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RE: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Wilson Nathan]

Here at Wisconsin we use a combination of DISP_ENC_TYPE and ADT_PAT_CLASS to 
determine what type of encounter it is/was.

DISP_ENC_TYPE determines if it is a hospital or non-hospital (visit, telephone, 
etc.) encounter and ADT_PAT_CLASS tells us what kind of hospital encounter we 
had (Inpatient, ED, etc.)

Nathan (the other one)

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Nathan Graham
Sent: Monday, August 25, 2014 8:31 AM
To: 'Supreet Kathpalia'; gpc-dev@listserv.kumc.edu
Cc: Tamara McMahon; Matthew Hoag
Subject: RE: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI

Supreet,

The Encounter Type in HERON does indeed come from ADT_PAT_CLASS – it’s a recent 
addition and is noted to be in “draft” status.  Perhaps there is another field 
we should be looking at.  Are you (or anyone else on the mailing list) aware of 
another way to get encounter type in Epic?

Regards,

Nathan

From: Supreet Kathpalia [mailto:budh0...@umn.edu]
Sent: Wednesday, August 20, 2014 4:34 PM
To: gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>
Cc: Campbell, James R; Nathan Graham
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI

We have initiated work on the ETL ADD at UMN and wondering how the counts are 
being generated for the encounter type.

Does there need to be consistency in our definition and mapping to each of the 
PCORI CDM encounter categories?( AV = Ambulatory Visit, ED = Emergency 
Department, IP = Inpatient Hospital Stay, IS = Non-Acute Institutional Stay, OA 
= Other Ambulatory Visit and others)

For the Epic sites, we could select certain encounter types to map to of the 
categories listed and thats the approach we started out with...

However, in looking at the PCORI- Annotated-Data Dictionary/heron_to_pcori.csv 
on bitbucket and the hierarchy on babel for KUMC it appears the ADT_PAT_CLASS 
is being mapped to the PCORI CDM encounter categories.

What is the standardized way to define the encounter type in order to generate 
counts across all sites?

Thanks and Regards,

Supreet

On Tue, Aug 19, 2014 at 10:53 AM, Nathan Graham 
mailto:ngra...@kumc.edu>> wrote:
All,

I’ll try to respond to some of the questions from Phillip and Lindsay based on 
the approach we at KU have taken so far.  Of course, this approach may not be 
optimal (and, I’m not done yet) so I’m eager for input from the group.

Phillip: “What is the current proposal for how the counts should be generated?”

-  I don’t know that we’ve decided as a network – please correct me if 
I’m wrong.  However, as suggested by 
Dan<https://informatics.gpcnetwork.org/trac/Project/ticket/145#comment:3>, I’ve 
tried to first map the i2b2-style paths for the PCORI CDM to the i2b2 paths we 
have in our i2b2 instance at KU (HERON).  Then from there, I tried to build 
views that look like the Common Data Model Specification from 
PCORI<http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20140319/da2b9f05/attachment-0001.docx>.
  I then generate the counts requested in PCORnet ETL Annotated Data Dictionary 
V1.0.xlsx<https://informatics.gpcnetwork.org/trac/Project/raw-attachment/ticket/144/PCORnet%20ETL%20Annotated%20Data%20Dictionary%20V1.0.xlsx>
 by querying against the CDM views.  The idea was that we could share much of 
the code across the network changing the mapping between the i2b2 path for 
PCORI CDM and local terminology.  I’ve made some progress with this approach 
(see pcori-annotated-data-dictionary project on 
BitBucket<https://bitbucket.org/njgraham/pcori-annotated-data-dictionary>) but 
I’m not done yet.

Phillip: “Nathan just sent an email about materializing the PCORI CDM view of 
the data warehouse.  Should we all plan to do this so that we will have a 
consistent process for generating the counts?”

-  I ran in to performance issues using the views and decided it would 
be better to just create CDM tables.  So far this is working better.  I don’t 
know if we should all take the materialized approach or not – I did it out of 
necessity.  I suspect others may experience similar performance issues using 
the view approach but I don’t know.  I’m not sure it matters if we all do 
exactly the same thing as long as we can support queries against CDM-shaped 
data.

Phillip:   “Will we be populating the CDM with all patients, regardless of the 
two visits requirement?  Historic data?  Etc?“

-  So far, I’ve taken the approach of counting all patients we have in 
i2b2.  As I recall, the “two visit in the past 30 day” constraint was for 
answering the “enrollment” questions on earlier PCORI characterization 
questions (since I don’t think we didn’t have firm guidance from PCORI on what 
enrollment means for a CDRN).  I’m not sure if we should add these constraints 
or not - the ETL Annotated Data Dictionary spreadsheet says:  “The purpose of 
this f

RE: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Nathan Graham]

Supreet,

The Encounter Type in HERON does indeed come from ADT_PAT_CLASS – it’s a recent 
addition and is noted to be in “draft” status.  Perhaps there is another field 
we should be looking at.  Are you (or anyone else on the mailing list) aware of 
another way to get encounter type in Epic?

Regards,

Nathan

From: Supreet Kathpalia [mailto:budh0...@umn.edu]
Sent: Wednesday, August 20, 2014 4:34 PM
To: gpc-dev@listserv.kumc.edu
Cc: Campbell, James R; Nathan Graham
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI

We have initiated work on the ETL ADD at UMN and wondering how the counts are 
being generated for the encounter type.

Does there need to be consistency in our definition and mapping to each of the 
PCORI CDM encounter categories?( AV = Ambulatory Visit, ED = Emergency 
Department, IP = Inpatient Hospital Stay, IS = Non-Acute Institutional Stay, OA 
= Other Ambulatory Visit and others)

For the Epic sites, we could select certain encounter types to map to of the 
categories listed and thats the approach we started out with...

However, in looking at the PCORI- Annotated-Data Dictionary/heron_to_pcori.csv 
on bitbucket and the hierarchy on babel for KUMC it appears the ADT_PAT_CLASS 
is being mapped to the PCORI CDM encounter categories.

What is the standardized way to define the encounter type in order to generate 
counts across all sites?

Thanks and Regards,

Supreet

On Tue, Aug 19, 2014 at 10:53 AM, Nathan Graham 
mailto:ngra...@kumc.edu>> wrote:
All,

I’ll try to respond to some of the questions from Phillip and Lindsay based on 
the approach we at KU have taken so far.  Of course, this approach may not be 
optimal (and, I’m not done yet) so I’m eager for input from the group.

Phillip: “What is the current proposal for how the counts should be generated?”

-  I don’t know that we’ve decided as a network – please correct me if 
I’m wrong.  However, as suggested by 
Dan<https://informatics.gpcnetwork.org/trac/Project/ticket/145#comment:3>, I’ve 
tried to first map the i2b2-style paths for the PCORI CDM to the i2b2 paths we 
have in our i2b2 instance at KU (HERON).  Then from there, I tried to build 
views that look like the Common Data Model Specification from 
PCORI<http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20140319/da2b9f05/attachment-0001.docx>.
  I then generate the counts requested in PCORnet ETL Annotated Data Dictionary 
V1.0.xlsx<https://informatics.gpcnetwork.org/trac/Project/raw-attachment/ticket/144/PCORnet%20ETL%20Annotated%20Data%20Dictionary%20V1.0.xlsx>
 by querying against the CDM views.  The idea was that we could share much of 
the code across the network changing the mapping between the i2b2 path for 
PCORI CDM and local terminology.  I’ve made some progress with this approach 
(see pcori-annotated-data-dictionary project on 
BitBucket<https://bitbucket.org/njgraham/pcori-annotated-data-dictionary>) but 
I’m not done yet.

Phillip: “Nathan just sent an email about materializing the PCORI CDM view of 
the data warehouse.  Should we all plan to do this so that we will have a 
consistent process for generating the counts?”

-  I ran in to performance issues using the views and decided it would 
be better to just create CDM tables.  So far this is working better.  I don’t 
know if we should all take the materialized approach or not – I did it out of 
necessity.  I suspect others may experience similar performance issues using 
the view approach but I don’t know.  I’m not sure it matters if we all do 
exactly the same thing as long as we can support queries against CDM-shaped 
data.

Phillip:   “Will we be populating the CDM with all patients, regardless of the 
two visits requirement?  Historic data?  Etc?“

-  So far, I’ve taken the approach of counting all patients we have in 
i2b2.  As I recall, the “two visit in the past 30 day” constraint was for 
answering the “enrollment” questions on earlier PCORI characterization 
questions (since I don’t think we didn’t have firm guidance from PCORI on what 
enrollment means for a CDRN).  I’m not sure if we should add these constraints 
or not - the ETL Annotated Data Dictionary spreadsheet says:  “The purpose of 
this form is to provide a mechanism for PCORnet data partners to communicate 
information about how they transformed their local data into the PCORnet Common 
Data Model (CDM) Version 1.0.” so I was just taking the approach of counting 
everything we ETL for now.

Lindsay: “I think that the Enrollment Table is one of the biggest question 
marks in my mind.  What do we plan on using for this table?”

-  I haven’t done anything yet.  In the notes from the gpc-dev call on 
July 
29<http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20140730/98039483/attachment-0001.pdf>,
 Jim Campbell noted that PCORI hasn’t clearly defined it yet and we can bypass 
until we get better guidance.  I don’t remember 

Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by campbell):

 I asked DSSNI about the "Table description" section of the ETL ADD
 worksheets.  Here is the reply:

 

 "The 'XXX Table Description' sections for each ETL Annotated Data
 Dictionary table/tab should include any details about the source data
 transformation to the PCORnet CDM, notes specific to the data source (e.g.
 the drop in age group X is real and is due to XYZ), and information about
 the data provider (e.g. included in this data are members who have medical
 coverage).  This type of information will allow the coordinating center to
 understand the usability of different data sources for specific projects
 and to understand data characteristics that might seem odd without
 understanding the data source details."
 

 Jim

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RE: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Wilson Nathan]

You can go ahead and load Wisconsin's as well

-Original Message-
From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
Sent: Monday, August 18, 2014 8:12 AM
To: campb...@unmc.edu; ngra...@kumc.edu; dconno...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by campbell):

 Jim>>>
 It appears that the listserv is not keeping everyone in the loop so I copy  
notes from Glen and Lindsay below.  Remember that the deliverable for the  ETL 
ADD at this point is supposedly on or about 9/15/2014.

 Nathan and Glen,
 Can I load your works in progress onto this ticket anticipating that we  will 
collate all our ETLADDs here?  That would allow other sites to review  what 
each other has done?

 Dan,
 Can you book extra time for tomorrows call and place the ETLADD discussion  
last on the agenda so we can spend some time reviewing the documents in  
whatever details is needed to guide all our sites.
 Jim

 Glenn>>>
 Jim, it appears that you are the lead dentist pulling teeth on this item.
 I’ve attached the spreadsheet with the description section filled in.
 Please let me know if this appears to be the right track. I’ve started  work 
on the demographics, and will try to fill out as much as possible of  the 
entire workbook Monday in anticipation of the Tue phone call.

  Thank you.

  - Glenn

 Medical Informatics Senior Analyst
 CTSI – Clinical & Translational Science Institute
 gbus...@mcw.edu<mailto:gbus...@mcw.edu>
 (414) 805-7239






 Campbell, James R

 Hi Lindsay I am good with scheduling a time to just discuss the ETL ADD  since 
I suspect we may need more than an hour to work through everyone's  issues. Can 
I suggest that we add the item to the regular scheduled  Tuesday agenda and I 
will ask KU to add an extra



 Sat 8/16








 Lindsay Cowell [lindsay.cow...@utsouthwestern.edu]
 Actions





 To:





 Campbell, James R‎; Phillip Reeder ‎[phillip.ree...@utsouthwestern.edu]‎‎;
 Susan Morrison ‎[susan.morri...@utsouthwestern.edu]‎‎; Dipti Ranganathan  
‎[dipti.ranganat...@utsouthwestern.edu]‎


 Cc:gpc-dev@listserv.kumc.edu

 Saturday, August 16, 2014 3:53 PM

 You replied on 8/16/2014 10:10 PM.

 Lindsay>>>
 Hi Jim,

  The GPC team at UTSW met yesterday to work on completing the ETL  Annotated
  Data Dictionary.  We have many of the same questions now as we had when
  generating counts for the original count table.  We would like to request
  a call during which we attempt to agree across the 10 sites on a
  standardized way to generate the counts (or as close as possible).
  Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we
  need a separate time.

  Thank you,

  Lindsay

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:10>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Phillip Reeder]

t yet and we can bypass 
until we get better guidance.  I don’t remember seeing better guidance yet – 
please let me know if I missed it.



From: 
gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu> 
[mailto:gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>]
 On Behalf Of Lindsay Cowell
Sent: Tuesday, August 19, 2014 9:21 AM
To: Phillip Reeder
Cc: Dipti Ranganathan; 
gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>

Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI


On Aug 18, 2014, at 10:44 AM, Phillip Reeder 
mailto:phillip.ree...@utsouthwestern.edu>>
 wrote:


I think that the Enrollment Table is one of the biggest question marks in my 
mind.  What do we plan on using for this table?  PCORI is expecting a start 
date/end date for the enrollment of a patient in the dataset, so the two visits 
in 3 years definition doesn’t seem to applicable.   I’m assuming our basis 
would be algorithmic, since we don’t have regional isolation and don’t have 
insurance enrollment data.  What algorithm should we apply?  How will we store 
this in i2b2?

I think for us at UTSW we would use encounter based basis. (defined in the ETL 
spreadsheet)

Thanks


What is the current proposal for how the counts should be generated?  Nathan 
just sent an email about materializing the PCORI CDM view of the data 
warehouse.  Should we all plan to do this so that we will have a consistent 
process for generating the counts?  Will we be populating the CDM with all 
patients, regardless of the two visits requirement?  Historic data?  Etc?

Phillip

From: Dan Connolly mailto:dconno...@kumc.edu>>
Date: Sunday, August 17, 2014 at 1:15 AM
To: Lindsay Cowell 
mailto:lindsay.cow...@utsouthwestern.edu>>
Cc: Phillip Reeder 
mailto:phillip.ree...@utsouthwestern.edu>>, 
"gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" 
mailto:gpc-dev@listserv.kumc.edu>>, Dipti 
Ranganathan 
mailto:dipti.ranganat...@utsouthwestern.edu>>,
 Susan Morrison 
mailto:susan.morri...@utsouthwestern.edu>>, 
"Campbell, James R" mailto:campb...@unmc.edu>>
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI


Would you please point us to your earlier questions? Or give a couple examples? 
Let's try to get as much done between calls as we can.
On Aug 16, 2014 3:53 PM, Lindsay Cowell 
mailto:lindsay.cow...@utsouthwestern.edu>> 
wrote:
Hi Jim,

The GPC team at UTSW met yesterday to work on completing the ETL Annotated
Data Dictionary.  We have many of the same questions now as we had when
generating counts for the original count table.  We would like to request
a call during which we attempt to agree across the 10 sites on a
standardized way to generate the counts (or as close as possible).
Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we
need a separate time.

Thank you,

Lindsay



On 8/14/14, 10:17 PM, "Campbell, James R" 
mailto:campb...@unmc.edu>> wrote:

>Nathan
>I think that I have responsibility for this deliverable and so you can
>forward Wisconsin response as attachment to the ticket and I will monitor
>and collate for the network response to PCORI.
>Jim
>
>James R. Campbell MD
>campb...@unmc.edu<mailto:campb...@unmc.edu>
>Office: 402-559-7505
>Secretary: 402-559-7299
>Pager: 402-888-1230
>
>> On Aug 14, 2014, at 2:56 PM, "Wilson Nathan" 
>> mailto:nwil...@uwhealth.org>>
>>wrote:
>>
>> Where or to whom should I send the Wisconsin data dictionary?
>>
>> Nathan Wilson
>>
>> -Original Message-
>> From: 
>> gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>
>>[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
>> Sent: Thursday, August 07, 2014 1:17 PM
>> To: campb...@unmc.edu<mailto:campb...@unmc.edu>; 
>> ngra...@kumc.edu<mailto:ngra...@kumc.edu>; 
>> dconno...@kumc.edu<mailto:dconno...@kumc.edu>
>> Cc: gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>
>> Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form
>>required by PCORI
>>
>> #144: ETL Annotated Data Dictionary form required by PCORI
>> -+
>> Reporter:  campbell |   Owner:  ngraham
>> Type:  task |  Status:  assigned
>> Priority:  major|   Milestone:  popmednet
>> Component:  data-stds|  Resolution:
>> Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
>> Blocking:   |
>> -+

Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Supreet Kathpalia]

We have initiated work on the ETL ADD at UMN and wondering how the counts
are being generated for the encounter type.

Does there need to be consistency in our definition and mapping to each of
the PCORI CDM encounter categories?( AV = Ambulatory Visit, ED = Emergency
Department, IP = Inpatient Hospital Stay, IS = Non-Acute Institutional
Stay, OA = Other Ambulatory Visit and others)

For the Epic sites, we could select certain encounter types to map to of
the categories listed and thats the approach we started out with...

However, in looking at the PCORI- Annotated-Data
Dictionary/heron_to_pcori.csv on bitbucket and the hierarchy on babel for
KUMC it appears the ADT_PAT_CLASS is being mapped to the PCORI CDM
encounter categories.

What is the standardized way to define the encounter type in order to
generate counts across all sites?

Thanks and Regards,

Supreet

On Tue, Aug 19, 2014 at 10:53 AM, Nathan Graham  wrote:

>  All,
>
>
>
> I’ll try to respond to some of the questions from Phillip and Lindsay
> based on the approach we at KU have taken so far.  Of course, this approach
> may not be optimal (and, I’m not done yet) so I’m eager for input from the
> group.
>
>
>
> Phillip: “What is the current proposal for how the counts should be
> generated?”
>
> -  I don’t know that we’ve decided as a network – please correct
> me if I’m wrong.  However, as suggested by Dan
> <https://informatics.gpcnetwork.org/trac/Project/ticket/145#comment:3>,
> I’ve tried to first map the i2b2-style paths for the PCORI CDM to the i2b2
> paths we have in our i2b2 instance at KU (HERON).  Then from there, I tried
> to build views that look like the Common Data Model Specification from
> PCORI
> <http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20140319/da2b9f05/attachment-0001.docx>.
> I then generate the counts requested in PCORnet ETL Annotated Data
> Dictionary V1.0.xlsx
> <https://informatics.gpcnetwork.org/trac/Project/raw-attachment/ticket/144/PCORnet%20ETL%20Annotated%20Data%20Dictionary%20V1.0.xlsx>
> by querying against the CDM views.  The idea was that we could share much
> of the code across the network changing the mapping between the i2b2 path
> for PCORI CDM and local terminology.  I’ve made some progress with this
> approach (see pcori-annotated-data-dictionary project on BitBucket
> <https://bitbucket.org/njgraham/pcori-annotated-data-dictionary>) but I’m
> not done yet.
>
>
>
> Phillip: “Nathan just sent an email about materializing the PCORI CDM view
> of the data warehouse.  Should we all plan to do this so that we will have
> a consistent process for generating the counts?”
>
> -  I ran in to performance issues using the views and decided it
> would be better to just create CDM tables.  So far this is working better.
> I don’t know if we should all take the materialized approach or not – I did
> it out of necessity.  I suspect others may experience similar performance
> issues using the view approach but I don’t know.  I’m not sure it matters
> if we all do exactly the same thing as long as we can support queries
> against CDM-shaped data.
>
>
>
> Phillip:   “Will we be populating the CDM with all patients, regardless of
> the two visits requirement?  Historic data?  Etc?“
>
> -  So far, I’ve taken the approach of counting all patients we
> have in i2b2.  As I recall, the “two visit in the past 30 day” constraint
> was for answering the “enrollment” questions on earlier PCORI
> characterization questions (since I don’t think we didn’t have firm
> guidance from PCORI on what enrollment means for a CDRN).  I’m not sure if
> we should add these constraints or not - the ETL Annotated Data Dictionary
> spreadsheet says:  *“The purpose of this form is to provide a mechanism
> for PCORnet data partners to communicate information about how they
> transformed their local data into the PCORnet Common Data Model (CDM)
> Version 1.0.”* so I was just taking the approach of counting everything
> we ETL for now.
>
>
>
> Lindsay: “I think that the Enrollment Table is one of the biggest question
> marks in my mind.  What do we plan on using for this table?”
>
> -  I haven’t done anything yet.  In the notes from the gpc-dev
> call on July 29
> <http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20140730/98039483/attachment-0001.pdf>,
> Jim Campbell noted that PCORI hasn’t clearly defined it yet and we can
> bypass until we get better guidance.  I don’t remember seeing better
> guidance yet – please let me know if I missed it.
>
>
>
>
>
>
>
> *From:* gpc-dev-boun...@listserv.kumc.edu [mailto:
> gpc-dev-boun...@listserv.kumc.edu] *On Behalf Of *Lindsay Cowell
> *Sent:* Tuesday, August 19, 2014 9:21 A

RE: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Nathan Graham]

All,

I'll try to respond to some of the questions from Phillip and Lindsay based on 
the approach we at KU have taken so far.  Of course, this approach may not be 
optimal (and, I'm not done yet) so I'm eager for input from the group.

Phillip: "What is the current proposal for how the counts should be generated?"

-  I don't know that we've decided as a network - please correct me if 
I'm wrong.  However, as suggested by 
Dan<https://informatics.gpcnetwork.org/trac/Project/ticket/145#comment:3>, I've 
tried to first map the i2b2-style paths for the PCORI CDM to the i2b2 paths we 
have in our i2b2 instance at KU (HERON).  Then from there, I tried to build 
views that look like the Common Data Model Specification from 
PCORI<http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20140319/da2b9f05/attachment-0001.docx>.
  I then generate the counts requested in PCORnet ETL Annotated Data Dictionary 
V1.0.xlsx<https://informatics.gpcnetwork.org/trac/Project/raw-attachment/ticket/144/PCORnet%20ETL%20Annotated%20Data%20Dictionary%20V1.0.xlsx>
 by querying against the CDM views.  The idea was that we could share much of 
the code across the network changing the mapping between the i2b2 path for 
PCORI CDM and local terminology.  I've made some progress with this approach 
(see pcori-annotated-data-dictionary project on 
BitBucket<https://bitbucket.org/njgraham/pcori-annotated-data-dictionary>) but 
I'm not done yet.

Phillip: "Nathan just sent an email about materializing the PCORI CDM view of 
the data warehouse.  Should we all plan to do this so that we will have a 
consistent process for generating the counts?"

-  I ran in to performance issues using the views and decided it would 
be better to just create CDM tables.  So far this is working better.  I don't 
know if we should all take the materialized approach or not - I did it out of 
necessity.  I suspect others may experience similar performance issues using 
the view approach but I don't know.  I'm not sure it matters if we all do 
exactly the same thing as long as we can support queries against CDM-shaped 
data.

Phillip:   "Will we be populating the CDM with all patients, regardless of the 
two visits requirement?  Historic data?  Etc?"

-  So far, I've taken the approach of counting all patients we have in 
i2b2.  As I recall, the "two visit in the past 30 day" constraint was for 
answering the "enrollment" questions on earlier PCORI characterization 
questions (since I don't think we didn't have firm guidance from PCORI on what 
enrollment means for a CDRN).  I'm not sure if we should add these constraints 
or not - the ETL Annotated Data Dictionary spreadsheet says:  "The purpose of 
this form is to provide a mechanism for PCORnet data partners to communicate 
information about how they transformed their local data into the PCORnet Common 
Data Model (CDM) Version 1.0." so I was just taking the approach of counting 
everything we ETL for now.

Lindsay: "I think that the Enrollment Table is one of the biggest question 
marks in my mind.  What do we plan on using for this table?"

-  I haven't done anything yet.  In the notes from the gpc-dev call on 
July 
29<http://listserv.kumc.edu/pipermail/gpc-dev/attachments/20140730/98039483/attachment-0001.pdf>,
 Jim Campbell noted that PCORI hasn't clearly defined it yet and we can bypass 
until we get better guidance.  I don't remember seeing better guidance yet - 
please let me know if I missed it.



From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Lindsay Cowell
Sent: Tuesday, August 19, 2014 9:21 AM
To: Phillip Reeder
Cc: Dipti Ranganathan; gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI


On Aug 18, 2014, at 10:44 AM, Phillip Reeder 
mailto:phillip.ree...@utsouthwestern.edu>>
 wrote:


I think that the Enrollment Table is one of the biggest question marks in my 
mind.  What do we plan on using for this table?  PCORI is expecting a start 
date/end date for the enrollment of a patient in the dataset, so the two visits 
in 3 years definition doesn't seem to applicable.   I'm assuming our basis 
would be algorithmic, since we don't have regional isolation and don't have 
insurance enrollment data.  What algorithm should we apply?  How will we store 
this in i2b2?

I think for us at UTSW we would use encounter based basis. (defined in the ETL 
spreadsheet)

Thanks


What is the current proposal for how the counts should be generated?  Nathan 
just sent an email about materializing the PCORI CDM view of the data 
warehouse.  Should we all plan to do this so that we will have a consistent 
process for generating the counts?  Will we b

Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Lindsay Cowell]

On Aug 18, 2014, at 10:44 AM, Phillip Reeder 
mailto:phillip.ree...@utsouthwestern.edu>>
 wrote:

I think that the Enrollment Table is one of the biggest question marks in my 
mind.  What do we plan on using for this table?  PCORI is expecting a start 
date/end date for the enrollment of a patient in the dataset, so the two visits 
in 3 years definition doesn’t seem to applicable.   I’m assuming our basis 
would be algorithmic, since we don’t have regional isolation and don’t have 
insurance enrollment data.  What algorithm should we apply?  How will we store 
this in i2b2?

I think for us at UTSW we would use encounter based basis. (defined in the ETL 
spreadsheet)

Thanks

What is the current proposal for how the counts should be generated?  Nathan 
just sent an email about materializing the PCORI CDM view of the data 
warehouse.  Should we all plan to do this so that we will have a consistent 
process for generating the counts?  Will we be populating the CDM with all 
patients, regardless of the two visits requirement?  Historic data?  Etc?

Phillip

From: Dan Connolly mailto:dconno...@kumc.edu>>
Date: Sunday, August 17, 2014 at 1:15 AM
To: Lindsay Cowell 
mailto:lindsay.cow...@utsouthwestern.edu>>
Cc: Phillip Reeder 
mailto:phillip.ree...@utsouthwestern.edu>>, 
"gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" 
mailto:gpc-dev@listserv.kumc.edu>>, Dipti 
Ranganathan 
mailto:dipti.ranganat...@utsouthwestern.edu>>,
 Susan Morrison 
mailto:susan.morri...@utsouthwestern.edu>>, 
"Campbell, James R" mailto:campb...@unmc.edu>>
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI


Would you please point us to your earlier questions? Or give a couple examples? 
Let's try to get as much done between calls as we can.

On Aug 16, 2014 3:53 PM, Lindsay Cowell 
mailto:lindsay.cow...@utsouthwestern.edu>> 
wrote:
Hi Jim,

The GPC team at UTSW met yesterday to work on completing the ETL Annotated
Data Dictionary.  We have many of the same questions now as we had when
generating counts for the original count table.  We would like to request
a call during which we attempt to agree across the 10 sites on a
standardized way to generate the counts (or as close as possible).
Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we
need a separate time.

Thank you,

Lindsay



On 8/14/14, 10:17 PM, "Campbell, James R" 
mailto:campb...@unmc.edu>> wrote:

>Nathan
>I think that I have responsibility for this deliverable and so you can
>forward Wisconsin response as attachment to the ticket and I will monitor
>and collate for the network response to PCORI.
>Jim
>
>James R. Campbell MD
>campb...@unmc.edu<mailto:campb...@unmc.edu>
>Office: 402-559-7505
>Secretary: 402-559-7299
>Pager: 402-888-1230
>
>> On Aug 14, 2014, at 2:56 PM, "Wilson Nathan" 
>> mailto:nwil...@uwhealth.org>>
>>wrote:
>>
>> Where or to whom should I send the Wisconsin data dictionary?
>>
>> Nathan Wilson
>>
>> -Original Message-
>> From: 
>> gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>
>>[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
>> Sent: Thursday, August 07, 2014 1:17 PM
>> To: campb...@unmc.edu<mailto:campb...@unmc.edu>; 
>> ngra...@kumc.edu<mailto:ngra...@kumc.edu>; 
>> dconno...@kumc.edu<mailto:dconno...@kumc.edu>
>> Cc: gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>
>> Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form
>>required by PCORI
>>
>> #144: ETL Annotated Data Dictionary form required by PCORI
>> -+
>> Reporter:  campbell |   Owner:  ngraham
>> Type:  task |  Status:  assigned
>> Priority:  major|   Milestone:  popmednet
>> Component:  data-stds|  Resolution:
>> Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
>> Blocking:   |
>> -+
>>
>> Comment (by ngraham):
>>
>> I worked on adding the 
>> [https://bitbucket.org/njgraham/pcori-annotated-
>> data-dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e
>>diagnosis  CDM view] but ran in to performance issues - see
>>ticket:146#comment:5.  I  plan to spend a little time trying to tune the
>>query.
>>
>> --
>> Ticket URL:
>><http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:9>
>> gpc-informatics <http://informatics.gpcnetwork.org/>
>> Greater Plains Ne

Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by campbell):

 I have uploaded draft work by MCW and UNMC and will add UW when I hear
 from Nathan.

 We will discuss questions and problems with completing these reports on
 the call today
 Jim

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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RE: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Dan Connolly]

Records of our May 13 call say "JC to get clarification from PCORI" about 
Enrollment.

Any news, Jim?

-- 
Dan



From: Phillip Reeder [phillip.ree...@utsouthwestern.edu]

Sent: Monday, August 18, 2014 10:44 AM

To: Dan Connolly; Lindsay Cowell

Cc: gpc-dev@listserv.kumc.edu; Dipti Ranganathan; Susan Morrison; Campbell, 
James R

Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI









I think that the Enrollment Table is one of the biggest question marks in my 
mind.  What do we plan on using for this table?  PCORI is expecting a start 
date/end date for the enrollment of a patient in the dataset, so the two visits 
in 3 years definition
 doesn’t seem to applicable.   I’m assuming our basis would be algorithmic, 
since we don’t have regional isolation and don’t have insurance enrollment 
data.  What algorithm should we apply?  How will we store this in i2b2?





What is the current proposal for how the counts should be generated?  Nathan 
just sent an email about materializing the PCORI CDM view of the data 
warehouse.  Should we all plan to do this so that we will have a consistent 
process for generating the counts?
  Will we be populating the CDM with all patients, regardless of the two visits 
requirement?  Historic data?  Etc?  





Phillip







From: Dan Connolly 

Date: Sunday, August 17, 2014 at 1:15 AM

To: Lindsay Cowell 

Cc: Phillip Reeder ,
 "gpc-dev@listserv.kumc.edu" ,
 Dipti Ranganathan , Susan Morrison 
,
 "Campbell, James R" 

Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI














Would you please point us to your earlier questions? Or give a couple examples? 
Let's try to get as much done between calls as we can.

On Aug 16, 2014 3:53 PM, Lindsay Cowell 
 wrote:




Hi Jim,



The GPC team at UTSW met yesterday to work on completing the ETL Annotated

Data Dictionary.  We have many of the same questions now as we had when

generating counts for the original count table.  We would like to request

a call during which we attempt to agree across the 10 sites on a

standardized way to generate the counts (or as close as possible).

Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we

need a separate time.



Thank you,



Lindsay







On 8/14/14, 10:17 PM, "Campbell, James R"  wrote:



>Nathan

>I think that I have responsibility for this deliverable and so you can

>forward Wisconsin response as attachment to the ticket and I will monitor

>and collate for the network response to PCORI.

>Jim

>

>James R. Campbell MD

>campb...@unmc.edu

>Office: 402-559-7505

>Secretary: 402-559-7299

>Pager: 402-888-1230

>

>> On Aug 14, 2014, at 2:56 PM, "Wilson Nathan" 

>>wrote:

>>

>> Where or to whom should I send the Wisconsin data dictionary?

>>

>> Nathan Wilson

>>

>> -Original Message-

>> From: 
gpc-dev-boun...@listserv.kumc.edu

>>[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics

>> Sent: Thursday, August 07, 2014 1:17 PM

>> To: 
campb...@unmc.edu; 
ngra...@kumc.edu; 
dconno...@kumc.edu

>> Cc: 
gpc-dev@listserv.kumc.edu

>> Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form

>>required by PCORI

>>

>> #144: ETL Annotated Data Dictionary form required by PCORI

>> -+

>> Reporter:  campbell |   Owner:  ngraham

>> Type:  task |  Status:  assigned

>> Priority:  major|   Milestone:  popmednet

>> Component:  data-stds|  Resolution:

>> Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146

>> Blocking:   |

>> -+

>>

>> Comment (by ngraham):

>>

>> I worked on adding the [https://bitbucket.org/njgraham/pcori-annotated-

>> data-dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e

>>diagnosis  CDM view] but ran in to performance issues - see

>>ticket:146#comment:5.  I  plan to spend a little time trying to tune the

>>query.

>>

>> --

>> Ticket URL:

>><http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:9>

>> gpc-informatics <http://informatics.gpcnetwork.org/>

>> Greater Plains Network - Informatics

>> ___

>> Gpc-dev mailing list

>> 
Gpc-dev@listserv.kumc.edu

>> 
http://listserv.kumc.edu/mailman/listinfo/gpc-dev

>

>The information in this e-mail may be privileged and confidential,

>intended only for the use of the addressee(s) above. Any unauthorized use

>or disclos

Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Phillip Reeder]

I think that the Enrollment Table is one of the biggest question marks in my 
mind.  What do we plan on using for this table?  PCORI is expecting a start 
date/end date for the enrollment of a patient in the dataset, so the two visits 
in 3 years definition doesn’t seem to applicable.   I’m assuming our basis 
would be algorithmic, since we don’t have regional isolation and don’t have 
insurance enrollment data.  What algorithm should we apply?  How will we store 
this in i2b2?

What is the current proposal for how the counts should be generated?  Nathan 
just sent an email about materializing the PCORI CDM view of the data 
warehouse.  Should we all plan to do this so that we will have a consistent 
process for generating the counts?  Will we be populating the CDM with all 
patients, regardless of the two visits requirement?  Historic data?  Etc?

Phillip

From: Dan Connolly mailto:dconno...@kumc.edu>>
Date: Sunday, August 17, 2014 at 1:15 AM
To: Lindsay Cowell 
mailto:lindsay.cow...@utsouthwestern.edu>>
Cc: Phillip Reeder 
mailto:phillip.ree...@utsouthwestern.edu>>, 
"gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" 
mailto:gpc-dev@listserv.kumc.edu>>, Dipti 
Ranganathan 
mailto:dipti.ranganat...@utsouthwestern.edu>>,
 Susan Morrison 
mailto:susan.morri...@utsouthwestern.edu>>, 
"Campbell, James R" mailto:campb...@unmc.edu>>
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI


Would you please point us to your earlier questions? Or give a couple examples? 
Let's try to get as much done between calls as we can.

On Aug 16, 2014 3:53 PM, Lindsay Cowell 
mailto:lindsay.cow...@utsouthwestern.edu>> 
wrote:
Hi Jim,

The GPC team at UTSW met yesterday to work on completing the ETL Annotated
Data Dictionary.  We have many of the same questions now as we had when
generating counts for the original count table.  We would like to request
a call during which we attempt to agree across the 10 sites on a
standardized way to generate the counts (or as close as possible).
Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we
need a separate time.

Thank you,

Lindsay



On 8/14/14, 10:17 PM, "Campbell, James R" 
mailto:campb...@unmc.edu>> wrote:

>Nathan
>I think that I have responsibility for this deliverable and so you can
>forward Wisconsin response as attachment to the ticket and I will monitor
>and collate for the network response to PCORI.
>Jim
>
>James R. Campbell MD
>campb...@unmc.edu<mailto:campb...@unmc.edu>
>Office: 402-559-7505
>Secretary: 402-559-7299
>Pager: 402-888-1230
>
>> On Aug 14, 2014, at 2:56 PM, "Wilson Nathan" 
>> mailto:nwil...@uwhealth.org>>
>>wrote:
>>
>> Where or to whom should I send the Wisconsin data dictionary?
>>
>> Nathan Wilson
>>
>> -Original Message-
>> From: 
>> gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>
>>[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
>> Sent: Thursday, August 07, 2014 1:17 PM
>> To: campb...@unmc.edu<mailto:campb...@unmc.edu>; 
>> ngra...@kumc.edu<mailto:ngra...@kumc.edu>; 
>> dconno...@kumc.edu<mailto:dconno...@kumc.edu>
>> Cc: gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>
>> Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form
>>required by PCORI
>>
>> #144: ETL Annotated Data Dictionary form required by PCORI
>> -+
>> Reporter:  campbell |   Owner:  ngraham
>> Type:  task |  Status:  assigned
>> Priority:  major|   Milestone:  popmednet
>> Component:  data-stds|  Resolution:
>> Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
>> Blocking:   |
>> -+
>>
>> Comment (by ngraham):
>>
>> I worked on adding the [https://bitbucket.org/njgraham/pcori-annotated-
>> data-dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e
>>diagnosis  CDM view] but ran in to performance issues - see
>>ticket:146#comment:5.  I  plan to spend a little time trying to tune the
>>query.
>>
>> --
>> Ticket URL:
>><http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:9>
>> gpc-informatics <http://informatics.gpcnetwork.org/>
>> Greater Plains Network - Informatics
>> ___
>> Gpc-dev mailing list
>> Gpc-dev@listserv.kumc.edu<mailto:Gpc-dev@listserv.kumc.edu>
>> http://listserv.kumc.

Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Bushee, Glenn]

No problem to upload. I was just sending it off to you as a first review before 
uploading in case I was tackling it wrong.

- Glenn

   Medical Informatics Senior Analyst
   CTSI – Clinical & Translational Science Institute
   gbus...@mcw.edu
   (414) 805-7239


From: GPC Informatics mailto:d...@madmode.com>>
Reply-To: "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" 
mailto:gpc-dev@listserv.kumc.edu>>
Date: Monday, August 18, 2014 at 8:12 AM
To: "campb...@unmc.edu<mailto:campb...@unmc.edu>" 
mailto:campb...@unmc.edu>>, 
"ngra...@kumc.edu<mailto:ngra...@kumc.edu>" 
mailto:ngra...@kumc.edu>>, 
"dconno...@kumc.edu<mailto:dconno...@kumc.edu>" 
mailto:dconno...@kumc.edu>>
Cc: "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI

#144: ETL Annotated Data Dictionary form required by PCORI
-+
Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
Blocking:   |
-+

Comment (by campbell):

Jim>>>
It appears that the listserv is not keeping everyone in the loop so I copy
notes from Glen and Lindsay below.  Remember that the deliverable for the
ETL ADD at this point is supposedly on or about 9/15/2014.

Nathan and Glen,
Can I load your works in progress onto this ticket anticipating that we
will collate all our ETLADDs here?  That would allow other sites to review
what each other has done?

Dan,
Can you book extra time for tomorrows call and place the ETLADD discussion
last on the agenda so we can spend some time reviewing the documents in
whatever details is needed to guide all our sites.
Jim

Glenn>>>
Jim, it appears that you are the lead dentist pulling teeth on this item.
I’ve attached the spreadsheet with the description section filled in.
Please let me know if this appears to be the right track. I’ve started
work on the demographics, and will try to fill out as much as possible of
the entire workbook Monday in anticipation of the Tue phone call.

  Thank you.

  - Glenn

 Medical Informatics Senior Analyst
 CTSI – Clinical & Translational Science Institute
 gbus...@mcw.edu<mailto:gbus...@mcw.edu><mailto:gbus...@mcw.edu>
 (414) 805-7239






Campbell, James R

Hi Lindsay I am good with scheduling a time to just discuss the ETL ADD
since I suspect we may need more than an hour to work through everyone's
issues. Can I suggest that we add the item to the regular scheduled
Tuesday agenda and I will ask KU to add an extra



Sat 8/16








Lindsay Cowell 
[lindsay.cow...@utsouthwestern.edu<mailto:lindsay.cow...@utsouthwestern.edu>]
Actions





To:





Campbell, James R; Phillip Reeder 
[phillip.ree...@utsouthwestern.edu<mailto:phillip.ree...@utsouthwestern.edu>];
Susan Morrison 
[susan.morri...@utsouthwestern.edu<mailto:susan.morri...@utsouthwestern.edu>]; 
Dipti Ranganathan
[dipti.ranganat...@utsouthwestern.edu<mailto:dipti.ranganat...@utsouthwestern.edu>]


Cc:gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>

Saturday, August 16, 2014 3:53 PM

You replied on 8/16/2014 10:10 PM.

Lindsay>>>
Hi Jim,

  The GPC team at UTSW met yesterday to work on completing the ETL
Annotated
  Data Dictionary.  We have many of the same questions now as we had when
  generating counts for the original count table.  We would like to request
  a call during which we attempt to agree across the 10 sites on a
  standardized way to generate the counts (or as close as possible).
  Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we
  need a separate time.

  Thank you,

  Lindsay

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:10>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by ngraham):

 As noted in comment:9, I worked on adding the
 [https://bitbucket.org/njgraham/pcori-annotated-data-
 dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e diagnosis CDM
 view] but ran in to performance issues - see ticket:146#comment:5.

 After discussing with Dan and others on the team, we decided to
 materialize the CDM views for performance (trading space for speed).  I
 plan to change the views to tables and see if things work better.

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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RE: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Dan Connolly]

As I mentioned last week, I'm in a meeting (the LEK) all day, so I'm not 
preparing an agenda.

I expect we can go as long as we like; I've never seen gotomeeting cut off a 
meeting.

Officially reserving extra time looks challenging; Brittany is not only 
participating in today's LEK but organizing all the logistics, so I don't 
expect she has bandwidth to deal with this.

Meanwhile, I'll repeat my request to please get the discussion started in 
substance in email.

-- 
Dan


From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on 
behalf of Campbell, James R [campb...@unmc.edu]
Sent: Saturday, August 16, 2014 10:10 PM
To: Lindsay Cowell; gpc-dev@listserv.kumc.edu
Subject: RE: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI

Hi Lindsay
I am good with scheduling a time to just discuss the ETL ADD since I suspect we 
may need more than an hour to work through everyone's issues. Can I suggest 
that we add the item to the regular scheduled  Tuesday agenda and I will ask KU 
to add an extra hour onto the call?  We can flow over if we need the extra time 
to agree on standardization issues and I would hope we don't go into the last 
week of August with questions outstanding.

ETL managers or technical leads speak up to the listserv if this is a bad time
Jim


From: Lindsay Cowell [lindsay.cow...@utsouthwestern.edu]
Sent: Saturday, August 16, 2014 3:53 PM
To: Campbell, James R; Phillip Reeder; Susan Morrison; Dipti Ranganathan
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI

Hi Jim,

The GPC team at UTSW met yesterday to work on completing the ETL Annotated
Data Dictionary.  We have many of the same questions now as we had when
generating counts for the original count table.  We would like to request
a call during which we attempt to agree across the 10 sites on a
standardized way to generate the counts (or as close as possible).
Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we
need a separate time.

Thank you,

Lindsay



On 8/14/14, 10:17 PM, "Campbell, James R"  wrote:

>Nathan
>I think that I have responsibility for this deliverable and so you can
>forward Wisconsin response as attachment to the ticket and I will monitor
>and collate for the network response to PCORI.
>Jim
>
>James R. Campbell MD
>campb...@unmc.edu
>Office: 402-559-7505
>Secretary: 402-559-7299
>Pager: 402-888-1230
>
>> On Aug 14, 2014, at 2:56 PM, "Wilson Nathan" 
>>wrote:
>>
>> Where or to whom should I send the Wisconsin data dictionary?
>>
>> Nathan Wilson
>>
>> -Original Message-
>> From: gpc-dev-boun...@listserv.kumc.edu
>>[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
>> Sent: Thursday, August 07, 2014 1:17 PM
>> To: campb...@unmc.edu; ngra...@kumc.edu; dconno...@kumc.edu
>> Cc: gpc-dev@listserv.kumc.edu
>> Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form
>>required by PCORI
>>
>> #144: ETL Annotated Data Dictionary form required by PCORI
>> -+
>> Reporter:  campbell |   Owner:  ngraham
>> Type:  task |  Status:  assigned
>> Priority:  major|   Milestone:  popmednet
>> Component:  data-stds|  Resolution:
>> Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
>> Blocking:   |
>> -+
>>
>> Comment (by ngraham):
>>
>> I worked on adding the [https://bitbucket.org/njgraham/pcori-annotated-
>> data-dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e
>>diagnosis  CDM view] but ran in to performance issues - see
>>ticket:146#comment:5.  I  plan to spend a little time trying to tune the
>>query.
>>
>> --
>> Ticket URL:
>><http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:9>
>> gpc-informatics <http://informatics.gpcnetwork.org/>
>> Greater Plains Network - Informatics
>> ___
>> Gpc-dev mailing list
>> Gpc-dev@listserv.kumc.edu
>> http://listserv.kumc.edu/mailman/listinfo/gpc-dev
>
>The information in this e-mail may be privileged and confidential,
>intended only for the use of the addressee(s) above. Any unauthorized use
>or disclosure of this information is prohibited. If you have received
>this e-mail by mistake, please delete it and immediately contact the
>sender.
>
>___

Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by campbell):

 Jim>>>
 It appears that the listserv is not keeping everyone in the loop so I copy
 notes from Glen and Lindsay below.  Remember that the deliverable for the
 ETL ADD at this point is supposedly on or about 9/15/2014.

 Nathan and Glen,
 Can I load your works in progress onto this ticket anticipating that we
 will collate all our ETLADDs here?  That would allow other sites to review
 what each other has done?

 Dan,
 Can you book extra time for tomorrows call and place the ETLADD discussion
 last on the agenda so we can spend some time reviewing the documents in
 whatever details is needed to guide all our sites.
 Jim

 Glenn>>>
 Jim, it appears that you are the lead dentist pulling teeth on this item.
 I’ve attached the spreadsheet with the description section filled in.
 Please let me know if this appears to be the right track. I’ve started
 work on the demographics, and will try to fill out as much as possible of
 the entire workbook Monday in anticipation of the Tue phone call.

  Thank you.

  - Glenn

 Medical Informatics Senior Analyst
 CTSI – Clinical & Translational Science Institute
 gbus...@mcw.edu
 (414) 805-7239






 Campbell, James R

 Hi Lindsay I am good with scheduling a time to just discuss the ETL ADD
 since I suspect we may need more than an hour to work through everyone's
 issues. Can I suggest that we add the item to the regular scheduled
 Tuesday agenda and I will ask KU to add an extra



 Sat 8/16








 Lindsay Cowell [lindsay.cow...@utsouthwestern.edu]
 Actions





 To:





 Campbell, James R‎; Phillip Reeder ‎[phillip.ree...@utsouthwestern.edu]‎‎;
 Susan Morrison ‎[susan.morri...@utsouthwestern.edu]‎‎; Dipti Ranganathan
 ‎[dipti.ranganat...@utsouthwestern.edu]‎


 Cc:gpc-dev@listserv.kumc.edu

 Saturday, August 16, 2014 3:53 PM

 You replied on 8/16/2014 10:10 PM.

 Lindsay>>>
 Hi Jim,

  The GPC team at UTSW met yesterday to work on completing the ETL
 Annotated
  Data Dictionary.  We have many of the same questions now as we had when
  generating counts for the original count table.  We would like to request
  a call during which we attempt to agree across the 10 sites on a
  standardized way to generate the counts (or as close as possible).
  Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we
  need a separate time.

  Thank you,

  Lindsay

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
___
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Dan Connolly]

Would you please point us to your earlier questions? Or give a couple examples? 
Let's try to get as much done between calls as we can.

On Aug 16, 2014 3:53 PM, Lindsay Cowell  
wrote:
Hi Jim,

The GPC team at UTSW met yesterday to work on completing the ETL Annotated
Data Dictionary.  We have many of the same questions now as we had when
generating counts for the original count table.  We would like to request
a call during which we attempt to agree across the 10 sites on a
standardized way to generate the counts (or as close as possible).
Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we
need a separate time.

Thank you,

Lindsay



On 8/14/14, 10:17 PM, "Campbell, James R"  wrote:

>Nathan
>I think that I have responsibility for this deliverable and so you can
>forward Wisconsin response as attachment to the ticket and I will monitor
>and collate for the network response to PCORI.
>Jim
>
>James R. Campbell MD
>campb...@unmc.edu
>Office: 402-559-7505
>Secretary: 402-559-7299
>Pager: 402-888-1230
>
>> On Aug 14, 2014, at 2:56 PM, "Wilson Nathan" 
>>wrote:
>>
>> Where or to whom should I send the Wisconsin data dictionary?
>>
>> Nathan Wilson
>>
>> -Original Message-
>> From: gpc-dev-boun...@listserv.kumc.edu
>>[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
>> Sent: Thursday, August 07, 2014 1:17 PM
>> To: campb...@unmc.edu; ngra...@kumc.edu; dconno...@kumc.edu
>> Cc: gpc-dev@listserv.kumc.edu
>> Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form
>>required by PCORI
>>
>> #144: ETL Annotated Data Dictionary form required by PCORI
>> -+
>> Reporter:  campbell |   Owner:  ngraham
>> Type:  task |  Status:  assigned
>> Priority:  major|   Milestone:  popmednet
>> Component:  data-stds|  Resolution:
>> Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
>> Blocking:   |
>> -+
>>
>> Comment (by ngraham):
>>
>> I worked on adding the [https://bitbucket.org/njgraham/pcori-annotated-
>> data-dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e
>>diagnosis  CDM view] but ran in to performance issues - see
>>ticket:146#comment:5.  I  plan to spend a little time trying to tune the
>>query.
>>
>> --
>> Ticket URL:
>><http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:9>
>> gpc-informatics <http://informatics.gpcnetwork.org/>
>> Greater Plains Network - Informatics
>> ___
>> Gpc-dev mailing list
>> Gpc-dev@listserv.kumc.edu
>> http://listserv.kumc.edu/mailman/listinfo/gpc-dev
>
>The information in this e-mail may be privileged and confidential,
>intended only for the use of the addressee(s) above. Any unauthorized use
>or disclosure of this information is prohibited. If you have received
>this e-mail by mistake, please delete it and immediately contact the
>sender.
>
>___
>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] #144: ETL Annotated Data Dictionary form required by PCORI

[Campbell, James R]

Hi Lindsay
I am good with scheduling a time to just discuss the ETL ADD since I suspect we 
may need more than an hour to work through everyone's issues. Can I suggest 
that we add the item to the regular scheduled  Tuesday agenda and I will ask KU 
to add an extra hour onto the call?  We can flow over if we need the extra time 
to agree on standardization issues and I would hope we don't go into the last 
week of August with questions outstanding.

ETL managers or technical leads speak up to the listserv if this is a bad time
Jim


From: Lindsay Cowell [lindsay.cow...@utsouthwestern.edu]
Sent: Saturday, August 16, 2014 3:53 PM
To: Campbell, James R; Phillip Reeder; Susan Morrison; Dipti Ranganathan
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI

Hi Jim,

The GPC team at UTSW met yesterday to work on completing the ETL Annotated
Data Dictionary.  We have many of the same questions now as we had when
generating counts for the original count table.  We would like to request
a call during which we attempt to agree across the 10 sites on a
standardized way to generate the counts (or as close as possible).
Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we
need a separate time.

Thank you,

Lindsay



On 8/14/14, 10:17 PM, "Campbell, James R"  wrote:

>Nathan
>I think that I have responsibility for this deliverable and so you can
>forward Wisconsin response as attachment to the ticket and I will monitor
>and collate for the network response to PCORI.
>Jim
>
>James R. Campbell MD
>campb...@unmc.edu
>Office: 402-559-7505
>Secretary: 402-559-7299
>Pager: 402-888-1230
>
>> On Aug 14, 2014, at 2:56 PM, "Wilson Nathan" 
>>wrote:
>>
>> Where or to whom should I send the Wisconsin data dictionary?
>>
>> Nathan Wilson
>>
>> -Original Message-
>> From: gpc-dev-boun...@listserv.kumc.edu
>>[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
>> Sent: Thursday, August 07, 2014 1:17 PM
>> To: campb...@unmc.edu; ngra...@kumc.edu; dconno...@kumc.edu
>> Cc: gpc-dev@listserv.kumc.edu
>> Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form
>>required by PCORI
>>
>> #144: ETL Annotated Data Dictionary form required by PCORI
>> -+
>> Reporter:  campbell |   Owner:  ngraham
>> Type:  task |  Status:  assigned
>> Priority:  major|   Milestone:  popmednet
>> Component:  data-stds|  Resolution:
>> Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
>> Blocking:   |
>> -+
>>
>> Comment (by ngraham):
>>
>> I worked on adding the [https://bitbucket.org/njgraham/pcori-annotated-
>> data-dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e
>>diagnosis  CDM view] but ran in to performance issues - see
>>ticket:146#comment:5.  I  plan to spend a little time trying to tune the
>>query.
>>
>> --
>> Ticket URL:
>><http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:9>
>> gpc-informatics <http://informatics.gpcnetwork.org/>
>> Greater Plains Network - Informatics
>> ___
>> Gpc-dev mailing list
>> Gpc-dev@listserv.kumc.edu
>> http://listserv.kumc.edu/mailman/listinfo/gpc-dev
>
>The information in this e-mail may be privileged and confidential,
>intended only for the use of the addressee(s) above. Any unauthorized use
>or disclosure of this information is prohibited. If you have received
>this e-mail by mistake, please delete it and immediately contact the
>sender.
>
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Lindsay Cowell]

Hi Jim,

The GPC team at UTSW met yesterday to work on completing the ETL Annotated
Data Dictionary.  We have many of the same questions now as we had when
generating counts for the original count table.  We would like to request
a call during which we attempt to agree across the 10 sites on a
standardized way to generate the counts (or as close as possible).
Perhaps this can happen during the next two gpc-dev calls?  Or perhaps we
need a separate time.

Thank you,

Lindsay



On 8/14/14, 10:17 PM, "Campbell, James R"  wrote:

>Nathan
>I think that I have responsibility for this deliverable and so you can
>forward Wisconsin response as attachment to the ticket and I will monitor
>and collate for the network response to PCORI.
>Jim
>
>James R. Campbell MD
>campb...@unmc.edu
>Office: 402-559-7505
>Secretary: 402-559-7299
>Pager: 402-888-1230
>
>> On Aug 14, 2014, at 2:56 PM, "Wilson Nathan" 
>>wrote:
>>
>> Where or to whom should I send the Wisconsin data dictionary?
>>
>> Nathan Wilson
>>
>> -Original Message-
>> From: gpc-dev-boun...@listserv.kumc.edu
>>[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
>> Sent: Thursday, August 07, 2014 1:17 PM
>> To: campb...@unmc.edu; ngra...@kumc.edu; dconno...@kumc.edu
>> Cc: gpc-dev@listserv.kumc.edu
>> Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form
>>required by PCORI
>>
>> #144: ETL Annotated Data Dictionary form required by PCORI
>> -+
>> Reporter:  campbell |   Owner:  ngraham
>> Type:  task |  Status:  assigned
>> Priority:  major|   Milestone:  popmednet
>> Component:  data-stds|  Resolution:
>> Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
>> Blocking:   |
>> -+
>>
>> Comment (by ngraham):
>>
>> I worked on adding the [https://bitbucket.org/njgraham/pcori-annotated-
>> data-dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e
>>diagnosis  CDM view] but ran in to performance issues - see
>>ticket:146#comment:5.  I  plan to spend a little time trying to tune the
>>query.
>>
>> --
>> Ticket URL:
>><http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:9>
>> gpc-informatics <http://informatics.gpcnetwork.org/>
>> Greater Plains Network - Informatics
>> ___
>> Gpc-dev mailing list
>> Gpc-dev@listserv.kumc.edu
>> http://listserv.kumc.edu/mailman/listinfo/gpc-dev
>
>The information in this e-mail may be privileged and confidential,
>intended only for the use of the addressee(s) above. Any unauthorized use
>or disclosure of this information is prohibited. If you have received
>this e-mail by mistake, please delete it and immediately contact the
>sender.
>
>___
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>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] #144: ETL Annotated Data Dictionary form required by PCORI

[Campbell, James R]

Nathan
I think that I have responsibility for this deliverable and so you can forward 
Wisconsin response as attachment to the ticket and I will monitor and collate 
for the network response to PCORI.
Jim

James R. Campbell MD
campb...@unmc.edu
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230

> On Aug 14, 2014, at 2:56 PM, "Wilson Nathan"  wrote:
>
> Where or to whom should I send the Wisconsin data dictionary?
>
> Nathan Wilson
>
> -Original Message-
> From: gpc-dev-boun...@listserv.kumc.edu 
> [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
> Sent: Thursday, August 07, 2014 1:17 PM
> To: campb...@unmc.edu; ngra...@kumc.edu; dconno...@kumc.edu
> Cc: gpc-dev@listserv.kumc.edu
> Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
> required by PCORI
>
> #144: ETL Annotated Data Dictionary form required by PCORI
> -+
> Reporter:  campbell |   Owner:  ngraham
> Type:  task |  Status:  assigned
> Priority:  major|   Milestone:  popmednet
> Component:  data-stds|  Resolution:
> Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
> Blocking:   |
> -+
>
> Comment (by ngraham):
>
> I worked on adding the [https://bitbucket.org/njgraham/pcori-annotated-
> data-dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e diagnosis  
> CDM view] but ran in to performance issues - see ticket:146#comment:5.  I  
> plan to spend a little time trying to tune the query.
>
> --
> Ticket URL: 
> <http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:9>
> gpc-informatics <http://informatics.gpcnetwork.org/>
> Greater Plains Network - Informatics
> ___
> Gpc-dev mailing list
> Gpc-dev@listserv.kumc.edu
> http://listserv.kumc.edu/mailman/listinfo/gpc-dev

The information in this e-mail may be privileged and confidential, intended 
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of this information is prohibited. If you have received this e-mail by mistake, 
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RE: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[Wilson Nathan]

Where or to whom should I send the Wisconsin data dictionary?

Nathan Wilson

-Original Message-
From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of GPC Informatics
Sent: Thursday, August 07, 2014 1:17 PM
To: campb...@unmc.edu; ngra...@kumc.edu; dconno...@kumc.edu
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form 
required by PCORI

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by ngraham):

 I worked on adding the [https://bitbucket.org/njgraham/pcori-annotated-
 data-dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e diagnosis  
CDM view] but ran in to performance issues - see ticket:146#comment:5.  I  plan 
to spend a little time trying to tune the query.

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:9>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by ngraham):

 I worked on adding the [https://bitbucket.org/njgraham/pcori-annotated-
 data-dictionary/commits/eb6e04281dfd9fd92758da1d51c7baf1d38e8e2e diagnosis
 CDM view] but ran in to performance issues - see ticket:146#comment:5.  I
 plan to spend a little time trying to tune the query.

--
Ticket URL: 

gpc-informatics 
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by dconnolly):

 Volunteers from July 29 call (#12) to fill out (at least) the
 "Description" tab:
  - DevTeams#uthscsa : Angela
  - DevTeams#wisc: Nathan Wilson
  - DevTeams#mcw: Glenn

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by campbell):

 We have ETL site managers identified for all sites except Iowa.

 All managers should review the edited ETL Annotated Data Dictionary that I
 have attached to this ticket and start to review content anticipating that
 they will need to supply information for all worksheets and we will need
 to respond to PCORI in September.

 Prakash, please respond with your designee
 Jim

--
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145, 146
 Blocking:   |
-+

Comment (by ngraham):

 I created a [https://bitbucket.org/njgraham/pcori-annotated-data-
 dictionary BitBucket repository] to keep track of the code created for
 this.  I haven't gotten too far yet, but started filling in CDM view for
 KUMC using [ticket:145#comment:3 Dan's example].

--
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  popmednet
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145
 Blocking:   |
-+
Changes (by dconnolly):

 * milestone:  data-stds-plan => popmednet


Comment:

 milestone:data-stds-plan (2.3) was submitted July 7.

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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+-
 Reporter:  campbell |   Owner:  ngraham
 Type:  task |  Status:  assigned
 Priority:  major|   Milestone:  data-stds-plan
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145
 Blocking:   |
-+-
Changes (by dconnolly):

 * owner:  dconnolly => ngraham
 * status:  new => assigned


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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
-+-
 Reporter:  campbell |   Owner:  dconnolly
 Type:  task |  Status:  new
 Priority:  major|   Milestone:  data-stds-plan
Component:  data-stds|  Resolution:
 Keywords:  ETL Data Dictionary  |  Blocked By:  145
 Blocking:   |
-+-

Old description:

> Note to DSSNI from Jenny Ibarra:
> >
> Attached is the PCORnet Extract, Transform, and Load (ETL) Annotated Data
> Dictionary. The purpose of this form is to provide a mechanism for
> PCORnet data partners to communicate information about how they
> transformed their local data into the PCORnet Common Data Model (CDM)
> Version 1.0. The information will be used to help the PCORnet
> Coordinating Center better understand the transformation process,
> appropriate uses of the PCORnet data, and the comparability of data
> sources. Please review the instructions found on the Overview tab before
> proceeding.
>
> You may contact the DSSNI Task force at ds...@pcornet.org for questions
> regarding completion of this form.
>
> We would like to identify a contact (organization/site, name, email) at
> each data source who will be coordinating the ETL process. Please send
> this contact information to ds...@pcornet.org by August 1.
> >

New description:

 Note to DSSNI from Jenny Ibarra:

 > Attached is the PCORnet Extract, Transform, and Load (ETL) Annotated
 Data Dictionary. The purpose of this form is to provide a mechanism for
 PCORnet data partners to communicate information about how they
 transformed their local data into the PCORnet Common Data Model (CDM)
 Version 1.0. The information will be used to help the PCORnet Coordinating
 Center better understand the transformation process, appropriate uses of
 the PCORnet data, and the comparability of data sources. Please review the
 instructions found on the Overview tab before proceeding.
 >
 > You may contact the DSSNI Task force at ds...@pcornet.org for questions
 regarding completion of this form.
 >
 > We would like to identify a contact (organization/site, name, email) at
 each data source who will be coordinating the ETL process. Please send
 this contact information to ds...@pcornet.org by August 1.

--

Comment (by dconnolly):

 Russ, we should talk about who should be our point person. I'm leaning
 towards Nathan (Graham).

 Meanwhile, it looks like each site will have to fill this out.

 It asks questions such as how many Unique PATIDs for a whole site, max
 ADMIT_DATE and so on. While we weren't planning to transform our whole
 datamart to CDM format, I can imagine, as part of work on #145 (transform
 i2b2 query results to PCORNet CDM), building views that would work for
 this purpose.

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[gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

[GPC Informatics]

#144: ETL Annotated Data Dictionary form required by PCORI
+-
  Reporter:  campbell   |  Owner:  dconnolly
  Type:  task   | Status:  new
  Priority:  major  |  Milestone:  data-stds-plan
 Component:  data-stds  |   Keywords:  ETL Data Dictionary
Blocked By: |   Blocking:
+-
 Note to DSSNI from Jenny Ibarra:
 >
 Attached is the PCORnet Extract, Transform, and Load (ETL) Annotated Data
 Dictionary. The purpose of this form is to provide a mechanism for PCORnet
 data partners to communicate information about how they transformed their
 local data into the PCORnet Common Data Model (CDM) Version 1.0. The
 information will be used to help the PCORnet Coordinating Center better
 understand the transformation process, appropriate uses of the PCORnet
 data, and the comparability of data sources. Please review the
 instructions found on the Overview tab before proceeding.

 You may contact the DSSNI Task force at ds...@pcornet.org for questions
 regarding completion of this form.

 We would like to identify a contact (organization/site, name, email) at
 each data source who will be coordinating the ETL process. Please send
 this contact information to ds...@pcornet.org by August 1.
 >

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