DSSNI phone call 8/25/14

[Campbell, James R]

My apologies to GPC colleagues that I did not make the call today.  I am taking 
a bit of sick leave and will be back on the job later in the week.  We had a 
PCORI DSSNI call Monday and I want to relate several items from that meeting:

1) CDM V2 will be released  this fall; they are very vague on the dates; may be 
as late as November but still uncertain

2) Enrollment class for CDM V1: the point of this is to identify population 
denominator by site;  they really want this info but are reluctant to dictate 
procedures; Brown emphasized  it is OK to take a flexible option as long as you 
document the methods you employ; PCORI would prefer that we try something…. I 
suggest we discuss this on our next call to try and standardize our approach 
across GPC.

3) Encounter Type AV should be used for ambulatory hospital surgery/procedure 
visits

4) SAS is likely to be a phase 2 requirement of CDRN networks although not for 
phase 1

5) Due date for ETLADD is shortly after milestone 2.7  “Within 4 months of 
award, initial set of data domains (as determined by Data S&I TF leadership) is 
harmonized within the CDRN” so our conclusion is that we must have ETLADD 
report ready by September 15!



Jim Campbell

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RE: ETL Annotated Dictionary Bug: Diagnosis Table includes many encounters with no diagnosis

[Nathan Graham]

Phillip / All,

Thanks for taking a look.  I think the issue is 
resolved
 - I used  'join' rather than a 'left join' as you suggested and then 
cross-checked the results with our fact counts in HERON and I think things are 
better now.

Thoughts?

Regards,

Nathan

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Nathan Graham
Sent: Tuesday, August 26, 2014 1:41 PM
To: GPC-DEV@LISTSERV.KUMC.EDU
Subject: ETL Annotated Dictionary Bug: Diagnosis Table includes many encounters 
with no diagnosis
Importance: High

Phillip,

As discussed, I'm forwarding to gpc-dev to continue the conversation regarding 
entries in the CDM diagnosis table with no diagnosis code (see ticket 
144 and Annotated 
Data Dictionary 
(BitBucket)).

I've created a bug report: "Diagnosis Table includes many encounters with no 
diagnosis".
  From just a quick look, it appears that we have many rows with NULL diagnosis 
at KU as well - I think I may want a join rather than a left join as you 
suggest.

Anyone can create issues (or at least that was my intent when configuring the 
BitBucket account).  I like feedback and want everyone to feel free to report 
issues or add comments, etc.  I wonder if it just adds more confusion to use 
the BitBucket bug tracker and also have the ticket on 
informatics.gpcnetwork.org.
  I guess we'll see how it goes...

Thanks.

Regards,

Nathan

From: Phillip Reeder [mailto:phillip.ree...@utsouthwestern.edu]
Sent: Tuesday, August 26, 2014 10:10 AM
To: Nathan Graham
Subject: i2b2 to PCORI
Importance: High

On line 418 of the CDM_transform.sql, you do a left join of the encounter table 
to the diagnosis.  For me, this is creating a ton of encounters that don't have 
an associated diagnosis.  I haven't tracked down why that is the case yet, but 
I'm guessing it has to do with some of our fake encounters we generate, along 
with unsynced encounters between systems and such.

Should this be a join instead  a left join, or possibly revers the order so 
that it is diagnosis left join encounter?  That way we would ensure that all 
rows had a non-null diagnosis.

And if for some reason, an encounter/visit didn't exist for the row, the 
diagnosis would still show up.

Thoughts?
Phillip





UT Southwestern Medical Center
The future of medicine, today.
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ETL Annotated Dictionary Bug: Diagnosis Table includes many encounters with no diagnosis

[Nathan Graham]

Phillip,

As discussed, I'm forwarding to gpc-dev to continue the conversation regarding 
entries in the CDM diagnosis table with no diagnosis code (see ticket 
144 and Annotated 
Data Dictionary 
(BitBucket)).

I've created a bug report: "Diagnosis Table includes many encounters with no 
diagnosis".
  From just a quick look, it appears that we have many rows with NULL diagnosis 
at KU as well - I think I may want a join rather than a left join as you 
suggest.

Anyone can create issues (or at least that was my intent when configuring the 
BitBucket account).  I like feedback and want everyone to feel free to report 
issues or add comments, etc.  I wonder if it just adds more confusion to use 
the BitBucket bug tracker and also have the ticket on 
informatics.gpcnetwork.org.
  I guess we'll see how it goes...

Thanks.

Regards,

Nathan

From: Phillip Reeder [mailto:phillip.ree...@utsouthwestern.edu]
Sent: Tuesday, August 26, 2014 10:10 AM
To: Nathan Graham
Subject: i2b2 to PCORI
Importance: High

On line 418 of the CDM_transform.sql, you do a left join of the encounter table 
to the diagnosis.  For me, this is creating a ton of encounters that don't have 
an associated diagnosis.  I haven't tracked down why that is the case yet, but 
I'm guessing it has to do with some of our fake encounters we generate, along 
with unsynced encounters between systems and such.

Should this be a join instead  a left join, or possibly revers the order so 
that it is diagnosis left join encounter?  That way we would ensure that all 
rows had a non-null diagnosis.

And if for some reason, an encounter/visit didn't exist for the row, the 
diagnosis would still show up.

Thoughts?
Phillip





UT Southwestern Medical Center
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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 
> Greater Plains Network - 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.

--
Ticket URL: 

gpc-informatics 
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GPC DEV meeting notes August 26th (GPC-DEV@listserv.kumc.edu)

[Supreet Kathpalia (via Google Docs)]

I've shared an item with you:

GPC DEV meeting notes August 26th
https://docs.google.com/document/d/1g77BNbADnSVy2wPoG5dpJiwqAVRiKZe1ufFT_mlZzT0/edit?usp=sharing&invite=CKuSgCs

It's not an attachment -- it's stored online. To open this item, just click  
the link above.


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Re: [gpc-informatics] #31: data elements for ALS cohort characterization

[GPC Informatics]

#31: data elements for ALS cohort characterization
-+
 Reporter:  dconnolly|   Owner:  jhe
 Type:  design-issue |  Status:  assigned
 Priority:  major|   Milestone:  data-agg1
Component:  data-stds|  Resolution:
 Keywords:  als-cohort methods-core  |  Blocked By:  63
 Blocking:   |
-+
Changes (by dconnolly):

 * cc: jhe@…, bokov, BPOLLOCK@…, rwaitman (removed)
 * cc: jhe (added)
 * owner:  rwaitman => jhe
 * milestone:  data-domains2 => data-agg1


Comment:

 Several of us met last Friday; unfortunately, Dr. Katz was out sick.
 Fortunately, we determined that he's not in the critical path for the next
 few steps.

 Dr. He is to work with Dr. Chen (and others?) to come up with a rough
 cohort characterization based on available data for review by Dr. Katz and
 others.

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Re: [gpc-informatics] #56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ...

[GPC Informatics]

#56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ...
--+
 Reporter:  dconnolly |   Owner:  bokov
 Type:  enhancement   |  Status:  assigned
 Priority:  major |   Milestone:  data-quality-plan
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:
 Blocking:|
--+
Changes (by dconnolly):

 * milestone:   => data-quality-plan


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Re: [gpc-informatics] #44: portable HERON ETL for NAACCR

[GPC Informatics]

#44: portable HERON ETL for NAACCR
-+
 Reporter:  dconnolly|   Owner:  dconnolly
 Type:  enhancement  |  Status:  assigned
 Priority:  major|   Milestone:  data-agg1
Component:  etl-dev  |  Resolution:
 Keywords:   |  Blocked By:
 Blocking:  119  |
-+
Changes (by dconnolly):

 * milestone:   => data-agg1


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Re: [gpc-informatics] #145: transform i2b2 query results to PCORNet CDM

[GPC Informatics]

#145: transform i2b2 query results to PCORNet CDM
--+---
 Reporter:  dconnolly |   Owner:  ngraham
 Type:  enhancement   |  Status:  assigned
 Priority:  major |   Milestone:  initial-data-domains
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  109
 Blocking:  144   |
--+---
Changes (by dconnolly):

 * milestone:  popmednet => initial-data-domains


Comment:

 cleaning up milestone:popmednet

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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: scribe volunteer for today?

[Supreet Kathpalia]

MN can be scribe today.

Thanks
Supreet

> On Aug 26, 2014, at 9:14 AM, Dan Connolly  wrote:
> 
> I'd like a vounteer, please.
> 
> Records (#12) show the groups yet to join the fun are UMN, UTHSCSA.
> 
> The nomination order after that is, based on most recent scribe service:
> 
> 
> Date   SiteScribe
> 5/6/2014   UIOWA  
> 5/20/2014  UTSW   
> 6/3/2014   CMH Nate Apathy
> 6/10/2014  KUMCNathan Graham
> 6/17/2014 
> CANCEL
> 6/24/2014  MCRFlv
> 7/1/2014   WISCTom Mish
> 7/15/2014  UNMCHubert Hickman
> 7/22/2014  CMH Nate Apathy
> 7/29/2014  KUMCNathan Graham
> 8/12/2014  WISCWilson Nathan
> 8/19/2014  MCW Kowalski, George
> Crossed out means there's a more recent occurrence.
> 
> -- 
> Dan
> 
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scribe volunteer for today?

[Dan Connolly]

I'd like a vounteer, please.

Records (#12) show 
the groups yet to join the fun are UMN, UTHSCSA.

The nomination order after that is, based on most recent scribe service:


DateSiteScribe
5/6/2014UIOWA

5/20/2014   UTSW

6/3/2014CMH Nate Apathy
6/10/2014   KUMCNathan Graham
6/17/2014
CANCEL
6/24/2014   MCRFlv
7/1/2014WISCTom Mish
7/15/2014   UNMCHubert Hickman
7/22/2014   CMH Nate Apathy
7/29/2014   KUMCNathan Graham
8/12/2014   WISCWilson Nathan
8/19/2014   MCW Kowalski, George

Crossed out means there's a more recent occurrence.

--
Dan

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