RE: Gather 2015 4th quarterly QA results

[Green, Timothy A.]

Thanks for sharing these. I am interested in an implementation agnostic QA 
process.  These scripts and the qa val list make a decent starting point to 
build some dynamic i2b2 queries that leverage the metadata layer.  As probably 
the only site with a vested interest in altering how the QA scripts work, I 
think it's fair for MU to take the lead on looking into it.

In the interim, we are going to focus on finishing our NAACCR load and then do 
something quick and dirty for the 2015/Q4 and 2016/Q1 QA results.


From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 3:10 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

Silly me... didn't give a URL in the first place:

regression test driver:
https://informatics.kumc.edu/work/browser/heron_load/test_heron_query.py

performance test driver:
https://informatics.kumc.edu/work/browser/heron_load/query_performance.py

The queries are captured this way:
https://informatics.kumc.edu/work/browser/heron_load/capture_query.py

The code is kinda... well... I'm not sure I'd write it that way today.

The gist of it is: we use capture_query.py to grab matching rows from 
qt_query_master and save (among other things) the I2B2_REQUEST_XML; then we 
make HTTP requests just like the web client would to log-in and replay the 
request.

--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 3:03 PM
To: Dan Connolly; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results
Indeed, I'm all for the forward looking approach.  What driver are you using 
for batch mode i2b2 queries?

From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 3:00 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

My first thought was: what does this have to do with the patient_dimension? It 
seems to only care what paths you use at your site.

But I think my tiny brain has finally absorbed the issue...

Even though our demographics ontology design is based on query paths, those 
query paths normally get looked up in the metadata table, which may say to look 
the path up in the concept_dimension, but may also say: we're done with the 
path; go look in some column of another dimension table.

This makes me wish we used more i2b2 queries for our QA stuff. I suppose we're 
headed that way with SHRINE/SNOW... Meanwhile, I wonder how many sites have the 
capacity to run a suite of i2b2 queries in lights-out fashon. We do this in the 
form performance and regression testing for HERON, but we should be able to 
straightforwardly adapt it for QA work.

That is to say: "some hard coded queries against patient_dimension" is one 
reasonable approach, but perhaps a more forward-looking approach would be some 
work-alike i2b2 queries.

--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 2:43 PM
To: Dan Connolly; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results
Yes, onboard with the readme, that is the other work we have to do, which is 
finding our paths that match the concept under QA.

Here is the same concept from the shared code, slightly different syntax.  I 
sent you a version we had already converted to mssql ourselves last December, 
before the code below was shared.  This can be found on line 95 here 
(https://bitbucket.org/gpcnetwork/gpc-qa-quarterly/src/e6d33c16e8691529f37025c36163bd3377d7e9e8/qa_mssql.sql?at=default&fileviewer=file-view-default).

select
v.VARIABLE_NAME
,count(distinct o.PATIENT_NUM) as RESULT
FROM $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_VAL_LIST] v
JOIN $(DataDB).[dbo].[CONCEPT_DIMENSION] c on (c.CONCEPT_PATH like 
v.CONCEPT_PATH_OR_CODE or c.concept_cd like v.CONCEPT_PATH_OR_CODE)
JOIN $(DataDB).[dbo].[OBSERVATION_FACT] o on o.concept_cd = c.concept_cd
JOIN  $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_ACTIVE_PATIENT] p on p.patient_num = 
o.patient_num
where v.POPULATION = 'Active'
and v.QUERY_TYPE = 'COUNT PATIENT'
group by v.variable_name




From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 2:19 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

Thanks for elaborating, but  I'm having trouble finding that statement in our 
shared code. "JOIN  #Q4_2015_GPC_QA_ACTIVE_PATIENT" doesn't occur in 
qa_mssql.sql
 of 2016-01-20 e6d33c16e869. nor does "QA_ACTIVE_TMP".

Are you referring to some previous versi

RE: Gather 2015 4th quarterly QA results

[Dan Connolly]

Silly me... didn't give a URL in the first place:

regression test driver:
https://informatics.kumc.edu/work/browser/heron_load/test_heron_query.py

performance test driver:
https://informatics.kumc.edu/work/browser/heron_load/query_performance.py

The queries are captured this way:
https://informatics.kumc.edu/work/browser/heron_load/capture_query.py

The code is kinda... well... I'm not sure I'd write it that way today.

The gist of it is: we use capture_query.py to grab matching rows from 
qt_query_master and save (among other things) the I2B2_REQUEST_XML; then we 
make HTTP requests just like the web client would to log-in and replay the 
request.

--
Dan


From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 3:03 PM
To: Dan Connolly; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

Indeed, I’m all for the forward looking approach.  What driver are you using 
for batch mode i2b2 queries?

From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 3:00 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

My first thought was: what does this have to do with the patient_dimension? It 
seems to only care what paths you use at your site.

But I think my tiny brain has finally absorbed the issue...

Even though our demographics ontology design is based on query paths, those 
query paths normally get looked up in the metadata table, which may say to look 
the path up in the concept_dimension, but may also say: we're done with the 
path; go look in some column of another dimension table.

This makes me wish we used more i2b2 queries for our QA stuff. I suppose we're 
headed that way with SHRINE/SNOW... Meanwhile, I wonder how many sites have the 
capacity to run a suite of i2b2 queries in lights-out fashon. We do this in the 
form performance and regression testing for HERON, but we should be able to 
straightforwardly adapt it for QA work.

That is to say: "some hard coded queries against patient_dimension" is one 
reasonable approach, but perhaps a more forward-looking approach would be some 
work-alike i2b2 queries.

--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 2:43 PM
To: Dan Connolly; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results
Yes, onboard with the readme, that is the other work we have to do, which is 
finding our paths that match the concept under QA.

Here is the same concept from the shared code, slightly different syntax.  I 
sent you a version we had already converted to mssql ourselves last December, 
before the code below was shared.  This can be found on line 95 here 
(https://bitbucket.org/gpcnetwork/gpc-qa-quarterly/src/e6d33c16e8691529f37025c36163bd3377d7e9e8/qa_mssql.sql?at=default&fileviewer=file-view-default).

select
v.VARIABLE_NAME
,count(distinct o.PATIENT_NUM) as RESULT
FROM $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_VAL_LIST] v
JOIN $(DataDB).[dbo].[CONCEPT_DIMENSION] c on (c.CONCEPT_PATH like 
v.CONCEPT_PATH_OR_CODE or c.concept_cd like v.CONCEPT_PATH_OR_CODE)
JOIN $(DataDB).[dbo].[OBSERVATION_FACT] o on o.concept_cd = c.concept_cd
JOIN  $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_ACTIVE_PATIENT] p on p.patient_num = 
o.patient_num
where v.POPULATION = 'Active'
and v.QUERY_TYPE = 'COUNT PATIENT'
group by v.variable_name




From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 2:19 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

Thanks for elaborating, but  I'm having trouble finding that statement in our 
shared code. "JOIN  #Q4_2015_GPC_QA_ACTIVE_PATIENT" doesn't occur in 
qa_mssql.sql
 of 2016-01-20 e6d33c16e869. nor does "QA_ACTIVE_TMP".

Are you referring to some previous version of the code? If so, which version?

Regarding editing val_list, I'm not entirely clear on how it works. I sort of 
naively hope that practice diminishes over time. The instructions in the 
REAME say:
For the script to return values, the columns titled "CONCEPT_PATH_OR_CODE" need 
to be updated with your organization's paths or codes. By default this column 
contains the paths or codes used in Babel. Do not edit the values in the 
"BABEL_PATH_OR_CODE" columns. These are used for reference to identify if your 
organization's path matches the babel path.
--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 1:54 PM
To: Thomas Mish; Dan Connolly; Mosa, Abu S.
Cc: McN

RE: Gather 2015 4th quarterly QA results

[Green, Timothy A.]

Indeed, I'm all for the forward looking approach.  What driver are you using 
for batch mode i2b2 queries?

From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 3:00 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

My first thought was: what does this have to do with the patient_dimension? It 
seems to only care what paths you use at your site.

But I think my tiny brain has finally absorbed the issue...

Even though our demographics ontology design is based on query paths, those 
query paths normally get looked up in the metadata table, which may say to look 
the path up in the concept_dimension, but may also say: we're done with the 
path; go look in some column of another dimension table.

This makes me wish we used more i2b2 queries for our QA stuff. I suppose we're 
headed that way with SHRINE/SNOW... Meanwhile, I wonder how many sites have the 
capacity to run a suite of i2b2 queries in lights-out fashon. We do this in the 
form performance and regression testing for HERON, but we should be able to 
straightforwardly adapt it for QA work.

That is to say: "some hard coded queries against patient_dimension" is one 
reasonable approach, but perhaps a more forward-looking approach would be some 
work-alike i2b2 queries.

--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 2:43 PM
To: Dan Connolly; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results
Yes, onboard with the readme, that is the other work we have to do, which is 
finding our paths that match the concept under QA.

Here is the same concept from the shared code, slightly different syntax.  I 
sent you a version we had already converted to mssql ourselves last December, 
before the code below was shared.  This can be found on line 95 here 
(https://bitbucket.org/gpcnetwork/gpc-qa-quarterly/src/e6d33c16e8691529f37025c36163bd3377d7e9e8/qa_mssql.sql?at=default&fileviewer=file-view-default).

select
v.VARIABLE_NAME
,count(distinct o.PATIENT_NUM) as RESULT
FROM $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_VAL_LIST] v
JOIN $(DataDB).[dbo].[CONCEPT_DIMENSION] c on (c.CONCEPT_PATH like 
v.CONCEPT_PATH_OR_CODE or c.concept_cd like v.CONCEPT_PATH_OR_CODE)
JOIN $(DataDB).[dbo].[OBSERVATION_FACT] o on o.concept_cd = c.concept_cd
JOIN  $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_ACTIVE_PATIENT] p on p.patient_num = 
o.patient_num
where v.POPULATION = 'Active'
and v.QUERY_TYPE = 'COUNT PATIENT'
group by v.variable_name




From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 2:19 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

Thanks for elaborating, but  I'm having trouble finding that statement in our 
shared code. "JOIN  #Q4_2015_GPC_QA_ACTIVE_PATIENT" doesn't occur in 
qa_mssql.sql
 of 2016-01-20 e6d33c16e869. nor does "QA_ACTIVE_TMP".

Are you referring to some previous version of the code? If so, which version?

Regarding editing val_list, I'm not entirely clear on how it works. I sort of 
naively hope that practice diminishes over time. The instructions in the 
REAME say:
For the script to return values, the columns titled "CONCEPT_PATH_OR_CODE" need 
to be updated with your organization's paths or codes. By default this column 
contains the paths or codes used in Babel. Do not edit the values in the 
"BABEL_PATH_OR_CODE" columns. These are used for reference to identify if your 
organization's path matches the babel path.
--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 1:54 PM
To: Thomas Mish; Dan Connolly; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results
Tom, thanks.  We've not yet started doing anything related to making it neutral 
with regards to location of patient attributes.  It's a tall order...I've taken 
a look at the way the i2b2 service layer builds it's queries.  It's fairly 
complex object oriented code that will be hard to adapt to straight SQL I think.

I think we will approach the first round with some hard coded queries against 
patient_dimension.

Dan:

This statement returns no results:
select v.VARIABLE_NAME ,count(distinct o.PATIENT_NUM) as RESULT
  into #Q4_2015_GPC_QA_ACTIVE_TMP
  FROM I2B2Data.Q4_2015_GPC_QA_VAL_LIST v
JOIN I2B2Data.CONCEPT_DIMENSION c on (c.CONCEPT_PATH like 
v.CONCEPT_PATH_OR_CODE or c.CONCEPT_CD like v.CONCEPT_PATH_OR_CODE)
JOIN I2B2Data.OBSERVATION_FACT o on o.concept_cd = c.concept_cd
   

Re: [gpc-informatics] #473: PCORnet CDMv3 SAS Readiness

[GPC Informatics]

#473: PCORnet CDMv3 SAS Readiness
---+
 Reporter:  lv |   Owner:  preeder
 Type:  task   |  Status:  assigned
 Priority:  major  |   Milestone:  gpc-phase2-h1
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:
 Blocking: |
---+

Comment (by dconnolly):

 Replying to [comment:17 nateapathy]:
 > Dan, where did you find NETWORK_ID and DATAMART_ID for your HARVEST
 table?

 That was Angela (comment:15).

 We (KUMC) don't (yet) have a HARVEST table (ref #476).

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
___
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev

RE: Gather 2015 4th quarterly QA results

[Dan Connolly]

My first thought was: what does this have to do with the patient_dimension? It 
seems to only care what paths you use at your site.

But I think my tiny brain has finally absorbed the issue...

Even though our demographics ontology design is based on query paths, those 
query paths normally get looked up in the metadata table, which may say to look 
the path up in the concept_dimension, but may also say: we're done with the 
path; go look in some column of another dimension table.

This makes me wish we used more i2b2 queries for our QA stuff. I suppose we're 
headed that way with SHRINE/SNOW... Meanwhile, I wonder how many sites have the 
capacity to run a suite of i2b2 queries in lights-out fashon. We do this in the 
form performance and regression testing for HERON, but we should be able to 
straightforwardly adapt it for QA work.

That is to say: "some hard coded queries against patient_dimension" is one 
reasonable approach, but perhaps a more forward-looking approach would be some 
work-alike i2b2 queries.

--
Dan


From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 2:43 PM
To: Dan Connolly; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

Yes, onboard with the readme, that is the other work we have to do, which is 
finding our paths that match the concept under QA.

Here is the same concept from the shared code, slightly different syntax.  I 
sent you a version we had already converted to mssql ourselves last December, 
before the code below was shared.  This can be found on line 95 here 
(https://bitbucket.org/gpcnetwork/gpc-qa-quarterly/src/e6d33c16e8691529f37025c36163bd3377d7e9e8/qa_mssql.sql?at=default&fileviewer=file-view-default).

select
v.VARIABLE_NAME
,count(distinct o.PATIENT_NUM) as RESULT
FROM $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_VAL_LIST] v
JOIN $(DataDB).[dbo].[CONCEPT_DIMENSION] c on (c.CONCEPT_PATH like 
v.CONCEPT_PATH_OR_CODE or c.concept_cd like v.CONCEPT_PATH_OR_CODE)
JOIN $(DataDB).[dbo].[OBSERVATION_FACT] o on o.concept_cd = c.concept_cd
JOIN  $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_ACTIVE_PATIENT] p on p.patient_num = 
o.patient_num
where v.POPULATION = 'Active'
and v.QUERY_TYPE = 'COUNT PATIENT'
group by v.variable_name




From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 2:19 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

Thanks for elaborating, but  I'm having trouble finding that statement in our 
shared code. "JOIN  #Q4_2015_GPC_QA_ACTIVE_PATIENT" doesn't occur in 
qa_mssql.sql
 of 2016-01-20 e6d33c16e869. nor does "QA_ACTIVE_TMP".

Are you referring to some previous version of the code? If so, which version?

Regarding editing val_list, I'm not entirely clear on how it works. I sort of 
naively hope that practice diminishes over time. The instructions in the 
REAME say:
For the script to return values, the columns titled "CONCEPT_PATH_OR_CODE" need 
to be updated with your organization's paths or codes. By default this column 
contains the paths or codes used in Babel. Do not edit the values in the 
"BABEL_PATH_OR_CODE" columns. These are used for reference to identify if your 
organization's path matches the babel path.
--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 1:54 PM
To: Thomas Mish; Dan Connolly; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results
Tom, thanks.  We’ve not yet started doing anything related to making it neutral 
with regards to location of patient attributes.  It’s a tall order…I’ve taken a 
look at the way the i2b2 service layer builds it’s queries.  It’s fairly 
complex object oriented code that will be hard to adapt to straight SQL I think.

I think we will approach the first round with some hard coded queries against 
patient_dimension.

Dan:

This statement returns no results:
select v.VARIABLE_NAME ,count(distinct o.PATIENT_NUM) as RESULT
  into #Q4_2015_GPC_QA_ACTIVE_TMP
  FROM I2B2Data.Q4_2015_GPC_QA_VAL_LIST v
JOIN I2B2Data.CONCEPT_DIMENSION c on (c.CONCEPT_PATH like 
v.CONCEPT_PATH_OR_CODE or c.CONCEPT_CD like v.CONCEPT_PATH_OR_CODE)
JOIN I2B2Data.OBSERVATION_FACT o on o.concept_cd = c.concept_cd
JOIN  #Q4_2015_GPC_QA_ACTIVE_PATIENT p on p.patient_num = o.patient_num
where v.POPULATION = 'Active'
and v.QUERY_TYPE = 'COUNT PATIENT'
group by v.variable_name;

We of course do have patients in our database, but this query assumes the 
information of interest is in observation_fact when it is in fact in 
patient_dimension in our database.

Regarding the ontol

Re: [gpc-informatics] #473: PCORnet CDMv3 SAS Readiness

[GPC Informatics]

#473: PCORnet CDMv3 SAS Readiness
---+
 Reporter:  lv |   Owner:  preeder
 Type:  task   |  Status:  assigned
 Priority:  major  |   Milestone:  gpc-phase2-h1
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:
 Blocking: |
---+

Comment (by nateapathy):

 > Replying to [comment:14 dconnolly]:
 > Per Russ's recommendation, we submitted our results as is (CDM v1.0
 compliance) after populating the Harvest table info. Here are the comments
 I added to PMN with our results:

 Dan, where did you find NETWORK_ID and DATAMART_ID for your HARVEST table?
 We are currently populating this data and I can't seem to find a resource
 for either of those fields. Is there a place on the Central Desktop where
 DSSNI assigned those values? I've looked on the QueryTool site, Central
 Desktop, gpc-dev and Trac and can't seem to find where we would obtain
 those values.

 Assuming this info will be valuable for other sites looking for this when
 they go to implement HARVEST.

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
___
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev

RE: Gather 2015 4th quarterly QA results

[Green, Timothy A.]

Yes, onboard with the readme, that is the other work we have to do, which is 
finding our paths that match the concept under QA.

Here is the same concept from the shared code, slightly different syntax.  I 
sent you a version we had already converted to mssql ourselves last December, 
before the code below was shared.  This can be found on line 95 here 
(https://bitbucket.org/gpcnetwork/gpc-qa-quarterly/src/e6d33c16e8691529f37025c36163bd3377d7e9e8/qa_mssql.sql?at=default&fileviewer=file-view-default).

select
v.VARIABLE_NAME
,count(distinct o.PATIENT_NUM) as RESULT
FROM $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_VAL_LIST] v
JOIN $(DataDB).[dbo].[CONCEPT_DIMENSION] c on (c.CONCEPT_PATH like 
v.CONCEPT_PATH_OR_CODE or c.concept_cd like v.CONCEPT_PATH_OR_CODE)
JOIN $(DataDB).[dbo].[OBSERVATION_FACT] o on o.concept_cd = c.concept_cd
JOIN  $(UtilitiesDB).[dbo].[Q3_2015_GPC_QA_ACTIVE_PATIENT] p on p.patient_num = 
o.patient_num
where v.POPULATION = 'Active'
and v.QUERY_TYPE = 'COUNT PATIENT'
group by v.variable_name




From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 2:19 PM
To: Green, Timothy A.; Thomas Mish; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

Thanks for elaborating, but  I'm having trouble finding that statement in our 
shared code. "JOIN  #Q4_2015_GPC_QA_ACTIVE_PATIENT" doesn't occur in 
qa_mssql.sql
 of 2016-01-20 e6d33c16e869. nor does "QA_ACTIVE_TMP".

Are you referring to some previous version of the code? If so, which version?

Regarding editing val_list, I'm not entirely clear on how it works. I sort of 
naively hope that practice diminishes over time. The instructions in the 
REAME say:
For the script to return values, the columns titled "CONCEPT_PATH_OR_CODE" need 
to be updated with your organization's paths or codes. By default this column 
contains the paths or codes used in Babel. Do not edit the values in the 
"BABEL_PATH_OR_CODE" columns. These are used for reference to identify if your 
organization's path matches the babel path.
--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 1:54 PM
To: Thomas Mish; Dan Connolly; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results
Tom, thanks.  We've not yet started doing anything related to making it neutral 
with regards to location of patient attributes.  It's a tall order...I've taken 
a look at the way the i2b2 service layer builds it's queries.  It's fairly 
complex object oriented code that will be hard to adapt to straight SQL I think.

I think we will approach the first round with some hard coded queries against 
patient_dimension.

Dan:

This statement returns no results:
select v.VARIABLE_NAME ,count(distinct o.PATIENT_NUM) as RESULT
  into #Q4_2015_GPC_QA_ACTIVE_TMP
  FROM I2B2Data.Q4_2015_GPC_QA_VAL_LIST v
JOIN I2B2Data.CONCEPT_DIMENSION c on (c.CONCEPT_PATH like 
v.CONCEPT_PATH_OR_CODE or c.CONCEPT_CD like v.CONCEPT_PATH_OR_CODE)
JOIN I2B2Data.OBSERVATION_FACT o on o.concept_cd = c.concept_cd
JOIN  #Q4_2015_GPC_QA_ACTIVE_PATIENT p on p.patient_num = o.patient_num
where v.POPULATION = 'Active'
and v.QUERY_TYPE = 'COUNT PATIENT'
group by v.variable_name;

We of course do have patients in our database, but this query assumes the 
information of interest is in observation_fact when it is in fact in 
patient_dimension in our database.

Regarding the ontology mapping, what I got from the instructions was to map our 
concept paths into the Q4_2015_GPC_QA_VAL_LIST file so it would return results. 
 Am I to understand that we should not be mapping our ontology paths to the 
Q4_2015_GPC_QA_VAL_LIST, but instead alter our metadata in i2b2 to match that 
which is in the base Q4_2015_GPC_QA_VAL_LIST file?


From: Thomas Mish [mailto:m...@wisc.edu]
Sent: Monday, February 15, 2016 12:17 PM
To: Dan Connolly; Green, Timothy A.; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

I think that very early on in the GPC conversations we covered a lot of ground 
in the fact vs patient dimension conversation. I know that here at Madison we 
altered the way we organized our i2b2 data at the time to that we were more 
like the rest of the GPC. I understand the angst over changing. I'd love to see 
what you doing/have done to make the script more neutral on this issues. We'll 
incorporate them as best as possible for next time to minimize the churn.

-TM

From: 
gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, February 15, 2016 11:50 AM
To: Green, Timoth

Re: gpc-dev 16 Feb agenda and meeting notes

[Justin Dale]

Related to #6, I would like to discuss how/why the UMN breast cancer cohort
had dates shifted twice.  This is related to ticket 470:
https://informatics.gpcnetwork.org/trac/Project/ticket/470


On Mon, Feb 15, 2016 at 1:22 PM, Dan Connolly  wrote:

> What else for tomorrow?
>
>- 16 Feb gpc-dev shared notes
>
> 
>
> current proposal:
> --
>
>
>1.
>
>Convene, take roll, review records and plan next meeting
>1.
>
>   ​Meeting ID and access code: 817-393-381
>   ; call +1
>   (571) 317-3131
>   2.
>
>   roll: all 12 DevTeams
>   
>   represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, 
> UTSW,
>   MU, IU
>   Reminder - put institution after your name in GoToMeeting
>   preferences
>   1.
>
>  today's scribe: George from MCW
>  2.
>
>  reminders from current work by owner site
>  :
>  (none)
>  1.
>
> MCW: #459 How to add GPC sites to SNOW SHRINE network?
> 
> - 28 Jan
> 2.
>
> MCW: #377 “George, SSDMF data sent - let me know how it
> goes.” - Feb 4
> 3.
>
> WISC: #327
>  
> Gather
> 2015 4th quarterly QA results (and 3rd quarter if feasible)
> 
> “Back to Tom to resume gathering results.” -- Jan 28
> 3.
>
>   comments on the agenda? on last week’s notes (#12
>   )? recent
>   tickets opened/closed
>    FYI
>   (note also recent ticket comments report
>   ):
>   1.
>
> none
> 4.
>
>   Next Meeting: 23 Feb Scribe: LRU nominates IU, MU, UNMC, UTSW, etc.
>   
>   2.
>
>milestone:adaptable-accrual
>
> 
>Feb 29
>1.
>
>   #273 
>   ADAPTABLE study ID linkage, REDCap integration - whiteboard design
>   discussion
>   2.
>
>   #462  
> validate
>   ADAPTABLE computable phenotype with chart review
>   
>   3.
>
>GPC Feasibility Query: Effects of Medicaid Expansion on Cancer Carein
>the United States
>   Tamara
>McMahon
>4.
>
>milestone:gpc-phase2-h1
>
>Feb 22
>1.
>
>   #473 PCORnet CDMv3 SAS Readiness
>    -
>   assigned to Reeder / UTSW
>   2.
>
>   #266 (CDM V3 Development for Phase 2) closed
>   
>   - dup
>   5.
>
>milestone:data-domains3
>
>March 28
>1.
>
>   #476 (SAS CDM v3 Diagnostic Query shows missing PROCEDURES table
>   etc.) created
>   
>   2.
>
>   #160  
> reproducible
>   GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4)
>   
>   1.
>
>  IN / LIKE limitation RE: SCILHS i2b2 to CDM on Oracle
>  
>Dan Connolly in reply to Reeder
>  2.
>
>  ethnicity conflated with race RE: SCILHS i2b2 to CDM on Oracle
>     Dan
>  Connolly in reply to Reeder
>  6.
>
>milestone:cohort-char-bc-db
>
> 
>1.
>
>   #475 (Invalid UIOWA value for NAACCR Item 3000) created
>   
>   accepted by Dan, FYI
>
> --
>
> --
> Dan
>
>
> ___
>

RE: Gather 2015 4th quarterly QA results

[Dan Connolly]

Thanks for elaborating, but  I'm having trouble finding that statement in our 
shared code. "JOIN  #Q4_2015_GPC_QA_ACTIVE_PATIENT" doesn't occur in 
qa_mssql.sql
 of 2016-01-20 e6d33c16e869. nor does "QA_ACTIVE_TMP".

Are you referring to some previous version of the code? If so, which version?

Regarding editing val_list, I'm not entirely clear on how it works. I sort of 
naively hope that practice diminishes over time. The instructions in the 
REAME say:
For the script to return values, the columns titled "CONCEPT_PATH_OR_CODE" need 
to be updated with your organization's paths or codes. By default this column 
contains the paths or codes used in Babel. Do not edit the values in the 
"BABEL_PATH_OR_CODE" columns. These are used for reference to identify if your 
organization's path matches the babel path.
--
Dan


From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 1:54 PM
To: Thomas Mish; Dan Connolly; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

Tom, thanks.  We’ve not yet started doing anything related to making it neutral 
with regards to location of patient attributes.  It’s a tall order…I’ve taken a 
look at the way the i2b2 service layer builds it’s queries.  It’s fairly 
complex object oriented code that will be hard to adapt to straight SQL I think.

I think we will approach the first round with some hard coded queries against 
patient_dimension.

Dan:

This statement returns no results:
select v.VARIABLE_NAME ,count(distinct o.PATIENT_NUM) as RESULT
  into #Q4_2015_GPC_QA_ACTIVE_TMP
  FROM I2B2Data.Q4_2015_GPC_QA_VAL_LIST v
JOIN I2B2Data.CONCEPT_DIMENSION c on (c.CONCEPT_PATH like 
v.CONCEPT_PATH_OR_CODE or c.CONCEPT_CD like v.CONCEPT_PATH_OR_CODE)
JOIN I2B2Data.OBSERVATION_FACT o on o.concept_cd = c.concept_cd
JOIN  #Q4_2015_GPC_QA_ACTIVE_PATIENT p on p.patient_num = o.patient_num
where v.POPULATION = 'Active'
and v.QUERY_TYPE = 'COUNT PATIENT'
group by v.variable_name;

We of course do have patients in our database, but this query assumes the 
information of interest is in observation_fact when it is in fact in 
patient_dimension in our database.

Regarding the ontology mapping, what I got from the instructions was to map our 
concept paths into the Q4_2015_GPC_QA_VAL_LIST file so it would return results. 
 Am I to understand that we should not be mapping our ontology paths to the 
Q4_2015_GPC_QA_VAL_LIST, but instead alter our metadata in i2b2 to match that 
which is in the base Q4_2015_GPC_QA_VAL_LIST file?


From: Thomas Mish [mailto:m...@wisc.edu]
Sent: Monday, February 15, 2016 12:17 PM
To: Dan Connolly; Green, Timothy A.; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

I think that very early on in the GPC conversations we covered a lot of ground 
in the fact vs patient dimension conversation. I know that here at Madison we 
altered the way we organized our i2b2 data at the time to that we were more 
like the rest of the GPC. I understand the angst over changing. I’d love to see 
what you doing/have done to make the script more neutral on this issues. We’ll 
incorporate them as best as possible for next time to minimize the churn.

-TM

From: 
gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, February 15, 2016 11:50 AM
To: Green, Timothy A. 
mailto:green...@health.missouri.edu>>; Mosa, Abu 
S. mailto:mo...@health.missouri.edu>>
Cc: McNeeley, Todd A. 
mailto:mcneele...@health.missouri.edu>>; 
mailto:gpc-dev@listserv.kumc.edu>> 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

To the extent that I did any of the writing of the QA scripts, I made no 
assumption about fact table vs. patient dimension. All our ontology design 
decisions regard paths. I haven't looked at all the code in detail, though. If 
there is such an assumption, it should be straightforward to refer us to one or 
more lines or statements that exhibit the assumption. Would you please give 
such details? Or just run the script and give us one or more diagnostic 
messages that show the assumption in action?

And as to "the relatively simple task of mapping..." that's the point of the QA 
scripts: to measure progress on that mapping. If you run the scripts and get 
some zeros, the script is still working correctly. It correctly shows that 
you're not finished. (You're not alone. KUMC has plenty of work to do in this 
area, for example.)

--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 10:38 AM
To: Mosa, Abu S.; Dan Connolly
Cc: mailto:gpc-d

RE: Gather 2015 4th quarterly QA results

[Green, Timothy A.]

Tom, thanks.  We've not yet started doing anything related to making it neutral 
with regards to location of patient attributes.  It's a tall order...I've taken 
a look at the way the i2b2 service layer builds it's queries.  It's fairly 
complex object oriented code that will be hard to adapt to straight SQL I think.

I think we will approach the first round with some hard coded queries against 
patient_dimension.

Dan:

This statement returns no results:
select v.VARIABLE_NAME ,count(distinct o.PATIENT_NUM) as RESULT
  into #Q4_2015_GPC_QA_ACTIVE_TMP
  FROM I2B2Data.Q4_2015_GPC_QA_VAL_LIST v
JOIN I2B2Data.CONCEPT_DIMENSION c on (c.CONCEPT_PATH like 
v.CONCEPT_PATH_OR_CODE or c.CONCEPT_CD like v.CONCEPT_PATH_OR_CODE)
JOIN I2B2Data.OBSERVATION_FACT o on o.concept_cd = c.concept_cd
JOIN  #Q4_2015_GPC_QA_ACTIVE_PATIENT p on p.patient_num = o.patient_num
where v.POPULATION = 'Active'
and v.QUERY_TYPE = 'COUNT PATIENT'
group by v.variable_name;

We of course do have patients in our database, but this query assumes the 
information of interest is in observation_fact when it is in fact in 
patient_dimension in our database.

Regarding the ontology mapping, what I got from the instructions was to map our 
concept paths into the Q4_2015_GPC_QA_VAL_LIST file so it would return results. 
 Am I to understand that we should not be mapping our ontology paths to the 
Q4_2015_GPC_QA_VAL_LIST, but instead alter our metadata in i2b2 to match that 
which is in the base Q4_2015_GPC_QA_VAL_LIST file?


From: Thomas Mish [mailto:m...@wisc.edu]
Sent: Monday, February 15, 2016 12:17 PM
To: Dan Connolly; Green, Timothy A.; Mosa, Abu S.
Cc: McNeeley, Todd A.; 
Subject: RE: Gather 2015 4th quarterly QA results

I think that very early on in the GPC conversations we covered a lot of ground 
in the fact vs patient dimension conversation. I know that here at Madison we 
altered the way we organized our i2b2 data at the time to that we were more 
like the rest of the GPC. I understand the angst over changing. I'd love to see 
what you doing/have done to make the script more neutral on this issues. We'll 
incorporate them as best as possible for next time to minimize the churn.

-TM

From: 
gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, February 15, 2016 11:50 AM
To: Green, Timothy A. 
mailto:green...@health.missouri.edu>>; Mosa, Abu 
S. mailto:mo...@health.missouri.edu>>
Cc: McNeeley, Todd A. 
mailto:mcneele...@health.missouri.edu>>; 
mailto:gpc-dev@listserv.kumc.edu>> 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

To the extent that I did any of the writing of the QA scripts, I made no 
assumption about fact table vs. patient dimension. All our ontology design 
decisions regard paths. I haven't looked at all the code in detail, though. If 
there is such an assumption, it should be straightforward to refer us to one or 
more lines or statements that exhibit the assumption. Would you please give 
such details? Or just run the script and give us one or more diagnostic 
messages that show the assumption in action?

And as to "the relatively simple task of mapping..." that's the point of the QA 
scripts: to measure progress on that mapping. If you run the scripts and get 
some zeros, the script is still working correctly. It correctly shows that 
you're not finished. (You're not alone. KUMC has plenty of work to do in this 
area, for example.)

--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 10:38 AM
To: Mosa, Abu S.; Dan Connolly
Cc: mailto:gpc-dev@listserv.kumc.edu>>; McNeeley, 
Todd A.
Subject: RE: Gather 2015 4th quarterly QA results
The patient demographics are stored in our i2b2 in the person dimension.  The 
QA scripts are written with the assumption that all data is stored in the fact 
table.  There is no provision for the script to leverage the ontology 
architecture to determine the storage location of the various pieces of data.  
I'm sure it was done that way to simplify the script, but it does ignore a 
pretty major feature of i2b2: the ontology mapping functionality.  This makes 
it less portable to sites that have a different implementation of the ontology. 
 I don't characterize a difference in implementation a problem in the data 
warehouse.

Keep in mind that MU had an i2b2 instance back in 2014, and the MU architecture 
was established before joining the GPC.  It would be work to either shift our 
demographics storage (and additional storage capacity), or to rewrite the QA 
scripts.  We will opt to rewrite the QA scripts, but to do it in a portable way 
(i.e. we could share our changes back to the GPC) will require some complexity 
of coding to leverage the ontology framework in i2b2.  We may have to opt for 
hardcoding our version against the dim

gpc-dev 16 Feb agenda and meeting notes

[Dan Connolly]

What else for tomorrow?

  *   16 Feb gpc-dev shared 
notes

current proposal:



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

 *   ​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

 *   roll: all 12 
DevTeams 
represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW, MU, IU
Reminder - put institution after your name in GoToMeeting preferences

*   today's scribe: George from MCW

*   reminders from current work by owner 
site: (none)

   *   MCW: #459 How to add GPC sites to SNOW SHRINE 
network? - 28 Jan

   *   MCW: #377 “George, SSDMF data sent - let me know how it goes.” - 
Feb 4

   *   WISC: 
#327 Gather 2015 
4th quarterly QA results (and 3rd quarter if 
feasible) “Back to 
Tom to resume gathering results.” -- Jan 28

 *   comments on the agenda? on last week’s notes 
(#12)? recent 
tickets opened/closed 
FYI (note also recent ticket comments 
report):

   *   none

 *   Next Meeting: 23 Feb Scribe: LRU nominates IU, MU, UNMC, UTSW, 
etc.

  2.  
milestone:adaptable-accrual
 Feb 29

 *   #273 
ADAPTABLE study ID linkage, REDCap integration - whiteboard design discussion

 *   #462 
validate ADAPTABLE computable phenotype with chart 
review

  3.  GPC Feasibility Query: Effects of Medicaid Expansion on Cancer Carein 
the United 
States   Tamara 
McMahon

  4.  
milestone:gpc-phase2-h1
 Feb 22

 *   #473 PCORnet CDMv3 SAS 
Readiness - 
assigned to Reeder / UTSW

 *   #266 (CDM V3 Development for Phase 2) 
closed - 
dup

  5.  
milestone:data-domains3
 March 28

 *   #476 (SAS CDM v3 Diagnostic Query shows missing PROCEDURES table etc.) 
created

 *   #160 
reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 
2.4)

*   IN / LIKE limitation RE: SCILHS i2b2 to CDM on 
Oracle   Dan 
Connolly in reply to Reeder

*   ethnicity conflated with race RE: SCILHS i2b2 to CDM on 
Oracle   Dan 
Connolly in reply to Reeder

  6.  
milestone:cohort-char-bc-db

 *   #475 (Invalid UIOWA value for NAACCR Item 3000) 
created accepted by 
Dan, FYI



--
Dan

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IN / LIKE limitation RE: SCILHS i2b2 to CDM on Oracle

[Dan Connolly]

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

--
Dan


From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on 
behalf of Phillip Reeder [phillip.ree...@utsouthwestern.edu]
Sent: Wednesday, February 10, 2016 12:12 PM
To: gpc-dev@listserv.kumc.edu
Subject: SCILHS i2b2 to CDM on Oracle

Has anyone else attempted the SCILHS i2b2 to CDM code on Oracle?  I’m focusing 
on the demographics table to start with have run into a few things I wanted to 
share.

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

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

Thanks,
Phillip





UT Southwestern


Medical Center



The future of medicine, today.

___
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Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev

ethnicity conflated with race RE: SCILHS i2b2 to CDM on Oracle

[Dan Connolly]

Re race/ethnicity #3, would you please open an i2p-transform 
issue?


--
Dan


From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on 
behalf of Phillip Reeder [phillip.ree...@utsouthwestern.edu]
Sent: Wednesday, February 10, 2016 12:12 PM
To: gpc-dev@listserv.kumc.edu
Subject: SCILHS i2b2 to CDM on Oracle

Has anyone else attempted the SCILHS i2b2 to CDM code on Oracle?  I’m focusing 
on the demographics table to start with have run into a few things I wanted to 
share.

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

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

Thanks,
Phillip





UT Southwestern


Medical Center



The future of medicine, today.

___
Gpc-dev mailing list
Gpc-dev@listserv.kumc.edu
http://listserv.kumc.edu/mailman/listinfo/gpc-dev

Re: [gpc-informatics] #473: PCORnet CDMv3 SAS Readiness

[GPC Informatics]

#473: PCORnet CDMv3 SAS Readiness
---+
 Reporter:  lv |   Owner:  preeder
 Type:  task   |  Status:  assigned
 Priority:  major  |   Milestone:  gpc-phase2-h1
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:
 Blocking: |
---+
Changes (by lv):

 * owner:  lv => preeder


Comment:

 Re-assigning to Phillip, based on the following communication:

 From: Darcy Louzao, Ph.D.
 Sent: Monday, February 15, 2016 12:21 PM
 To: Verhagen, Laurel A
 Cc: James Topping; Laura Qualls
 Subject: UTSW Med Ctr

 I believe UTSW Med Ctr is the only !DataMart that was sent the Diagnostic
 Query that we have not heard back from. Are they able to complete the
 query on CDM v3.0? If not, when is an anticipated new readiness date?

 Thank you,
 Darcy

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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RE: Gather 2015 4th quarterly QA results

[Thomas Mish]

I think that very early on in the GPC conversations we covered a lot of ground 
in the fact vs patient dimension conversation. I know that here at Madison we 
altered the way we organized our i2b2 data at the time to that we were more 
like the rest of the GPC. I understand the angst over changing. I'd love to see 
what you doing/have done to make the script more neutral on this issues. We'll 
incorporate them as best as possible for next time to minimize the churn.

-TM

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, February 15, 2016 11:50 AM
To: Green, Timothy A. ; Mosa, Abu S. 

Cc: McNeeley, Todd A. ; 
 
Subject: RE: Gather 2015 4th quarterly QA results

To the extent that I did any of the writing of the QA scripts, I made no 
assumption about fact table vs. patient dimension. All our ontology design 
decisions regard paths. I haven't looked at all the code in detail, though. If 
there is such an assumption, it should be straightforward to refer us to one or 
more lines or statements that exhibit the assumption. Would you please give 
such details? Or just run the script and give us one or more diagnostic 
messages that show the assumption in action?

And as to "the relatively simple task of mapping..." that's the point of the QA 
scripts: to measure progress on that mapping. If you run the scripts and get 
some zeros, the script is still working correctly. It correctly shows that 
you're not finished. (You're not alone. KUMC has plenty of work to do in this 
area, for example.)

--
Dan

From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 10:38 AM
To: Mosa, Abu S.; Dan Connolly
Cc: mailto:gpc-dev@listserv.kumc.edu>>; McNeeley, 
Todd A.
Subject: RE: Gather 2015 4th quarterly QA results
The patient demographics are stored in our i2b2 in the person dimension.  The 
QA scripts are written with the assumption that all data is stored in the fact 
table.  There is no provision for the script to leverage the ontology 
architecture to determine the storage location of the various pieces of data.  
I'm sure it was done that way to simplify the script, but it does ignore a 
pretty major feature of i2b2: the ontology mapping functionality.  This makes 
it less portable to sites that have a different implementation of the ontology. 
 I don't characterize a difference in implementation a problem in the data 
warehouse.

Keep in mind that MU had an i2b2 instance back in 2014, and the MU architecture 
was established before joining the GPC.  It would be work to either shift our 
demographics storage (and additional storage capacity), or to rewrite the QA 
scripts.  We will opt to rewrite the QA scripts, but to do it in a portable way 
(i.e. we could share our changes back to the GPC) will require some complexity 
of coding to leverage the ontology framework in i2b2.  We may have to opt for 
hardcoding our version against the dimension table.

Aside from that, we still have the relatively simple task of mapping our 
concept codes/paths to get the remainder (non-demographic part) of the script 
to work correctly.

Tim



From: Mosa, Abu S.
Sent: Monday, February 15, 2016 10:20 AM
To: Dan Connolly
Cc: mailto:gpc-dev@listserv.kumc.edu>>; Green, 
Timothy A.; McNeeley, Todd A.
Subject: RE: Gather 2015 4th quarterly QA results

I would defer this to Tim and Todd to share their thoughts on this. Thanks. 
--Mosa

From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 10:03 AM
To: Mosa, Abu S. mailto:mo...@health.missouri.edu>>
Cc: mailto:gpc-dev@listserv.kumc.edu>> 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

What are the symptoms when you try to run the QA scripts, Mosa? What 
diagnostics do you get?

The premise of the QA scripts is that if they don't run, that's a problem with 
your data warehouse. Perhaps there are actually problems with the scripts, but 
if so, we need details on what those problems are. Also, we have a shared 
source code repository in 
gpc-qa-quarterly. So if you 
make changes, please strive to make them portable to other sites.

p.s. I presume it's OK to share this thread with gpc-dev, as it regards group 
technical work.

--
Dan

From: Mosa, Abu S. [mo...@health.missouri.edu]
Sent: Friday, February 12, 2016 4:41 PM
To: Dan Connolly
Subject: Gather 2015 4th quarterly QA results
Hi Dan,

I talked with our technical team about generating the 2015 4th quarterly 
report. They looked into the MSSQL code that you referred to me on BitBucket. 
They advised that major re-writing effort is needed in order to localize the 
scripts to be able to run on our i2b2 data model. They are currently focusing 
on the Phase I implementation (specifically tumor registry data load) which 
they target to complete by end of this month. So

Re: [gpc-informatics] #473: PCORnet CDMv3 SAS Readiness

[GPC Informatics]

#473: PCORnet CDMv3 SAS Readiness
---+
 Reporter:  lv |   Owner:  lv
 Type:  task   |  Status:  assigned
 Priority:  major  |   Milestone:  gpc-phase2-h1
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:
 Blocking: |
---+
Changes (by bos):

 * owner:  bos => lv


Comment:

 Replying to [comment:14 dconnolly]:
 Per Russ's recommendation, we submitted our results as is (CDM v1.0
 compliance) after populating the Harvest table info. Here are the comments
 I added to PMN with our results:

 * GPC/UTHSCSA has CDM v1.0 for tables with data: demographic, diagnosis,
 encounter, enrollment, procedures, vital
 * Additional tables for CDM v3 have been created but not yet populated,
 except for the Harvest table
 * GPC/UTHSCSA is currently using algorithmic enrollment criteria of 2
 visits within the past 3 years at least 30 days apart.

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RE: Gather 2015 4th quarterly QA results

[Dan Connolly]

To the extent that I did any of the writing of the QA scripts, I made no 
assumption about fact table vs. patient dimension. All our ontology design 
decisions regard paths. I haven't looked at all the code in detail, though. If 
there is such an assumption, it should be straightforward to refer us to one or 
more lines or statements that exhibit the assumption. Would you please give 
such details? Or just run the script and give us one or more diagnostic 
messages that show the assumption in action?

And as to "the relatively simple task of mapping..." that's the point of the QA 
scripts: to measure progress on that mapping. If you run the scripts and get 
some zeros, the script is still working correctly. It correctly shows that 
you're not finished. (You're not alone. KUMC has plenty of work to do in this 
area, for example.)

--
Dan


From: Green, Timothy A. [green...@health.missouri.edu]
Sent: Monday, February 15, 2016 10:38 AM
To: Mosa, Abu S.; Dan Connolly
Cc: ; McNeeley, Todd A.
Subject: RE: Gather 2015 4th quarterly QA results

The patient demographics are stored in our i2b2 in the person dimension.  The 
QA scripts are written with the assumption that all data is stored in the fact 
table.  There is no provision for the script to leverage the ontology 
architecture to determine the storage location of the various pieces of data.  
I’m sure it was done that way to simplify the script, but it does ignore a 
pretty major feature of i2b2: the ontology mapping functionality.  This makes 
it less portable to sites that have a different implementation of the ontology. 
 I don’t characterize a difference in implementation a problem in the data 
warehouse.

Keep in mind that MU had an i2b2 instance back in 2014, and the MU architecture 
was established before joining the GPC.  It would be work to either shift our 
demographics storage (and additional storage capacity), or to rewrite the QA 
scripts.  We will opt to rewrite the QA scripts, but to do it in a portable way 
(i.e. we could share our changes back to the GPC) will require some complexity 
of coding to leverage the ontology framework in i2b2.  We may have to opt for 
hardcoding our version against the dimension table.

Aside from that, we still have the relatively simple task of mapping our 
concept codes/paths to get the remainder (non-demographic part) of the script 
to work correctly.

Tim



From: Mosa, Abu S.
Sent: Monday, February 15, 2016 10:20 AM
To: Dan Connolly
Cc: ; Green, Timothy A.; McNeeley, Todd A.
Subject: RE: Gather 2015 4th quarterly QA results

I would defer this to Tim and Todd to share their thoughts on this. Thanks. 
--Mosa

From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 10:03 AM
To: Mosa, Abu S. mailto:mo...@health.missouri.edu>>
Cc: mailto:gpc-dev@listserv.kumc.edu>> 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

What are the symptoms when you try to run the QA scripts, Mosa? What 
diagnostics do you get?

The premise of the QA scripts is that if they don't run, that's a problem with 
your data warehouse. Perhaps there are actually problems with the scripts, but 
if so, we need details on what those problems are. Also, we have a shared 
source code repository in 
gpc-qa-quarterly. So if you 
make changes, please strive to make them portable to other sites.

p.s. I presume it's OK to share this thread with gpc-dev, as it regards group 
technical work.

--
Dan

From: Mosa, Abu S. [mo...@health.missouri.edu]
Sent: Friday, February 12, 2016 4:41 PM
To: Dan Connolly
Subject: Gather 2015 4th quarterly QA results
Hi Dan,

I talked with our technical team about generating the 2015 4th quarterly 
report. They looked into the MSSQL code that you referred to me on BitBucket. 
They advised that major re-writing effort is needed in order to localize the 
scripts to be able to run on our i2b2 data model. They are currently focusing 
on the Phase I implementation (specifically tumor registry data load) which 
they target to complete by end of this month. So, a viable timeline for 
generating the 2015 4th quarterly report for us would be Mid-march. Let me know 
if you have any questions. If needed, we can discuss this during the next Dev 
call.

Regards,
Abu Saleh Mohammad Mosa, PhD
Director, Research Informatics
Institute for Clinical and Translational Science
University of Missouri


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Re: [gpc-informatics] #473: PCORnet CDMv3 SAS Readiness

[GPC Informatics]

#473: PCORnet CDMv3 SAS Readiness
---+
 Reporter:  lv |   Owner:  bos
 Type:  task   |  Status:  assigned
 Priority:  major  |   Milestone:  gpc-phase2-h1
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:
 Blocking: |
---+
Changes (by dconnolly):

 * owner:  lv => bos


Old description:

> ''Laurel reporting on behalf of Darcy Louzao:''
>
> Specifically, can you verify/update the date at which each data partner
> will be ready to receive the Diagnostic Query (DQ), for which the
> requirements are:
>
> • CDM v3.0 with SAS data types
> • All 15 tables present
> • Demographic, Enrollment, Encounter, Diagnosis, Procedures, Vital, and
> Harvest tables populated
>
> ||Site  ||SAS CDM v3 Readiness Date/DQ Status
> ||Children's Mercy  ||06/15/16
> ||Indiana U Regenstrief ||03/01/16
> ||Marshfield Clinic ||Completed DQ
> ||Med Coll Wisconsin||03/31/16
> ||U of Minnesota AHC||03/31/16
> ||U of Missouri HC  ||06/30/16
> ||U of Nebraska ||3/15/16
> ||University of Iowa||TBD
> ||University of Kansas  ||DQ sent 2/2/16
> ||UT San Antonio||DQ sent 2/2/16
> ||UT SW Med Ctr ||DQ sent 2/2/16
> ||UW Madison||03/14/16
>

>
> Additionally, please keep the following points in mind for future
> planning:
> 1. We will send the Diagnostic Query based on the dates you provide (I
> will check-in the week prior to sending to verify readiness)
> 2. We will request a response in ~2 weeks
> 3. Requirements for the next step, Data Characterization, are:
> • Successful diagnostic response, ie. no exceptions noted (in the
> workplan they are described as “unexpected conditions”)
> • Locked/static data
> • Will need to submit an ETL ADD with their query response (the template
> is on our Data Characterization wiki)

New description:

 ''Laurel reporting on behalf of Darcy Louzao:''

 Specifically, can you verify/update the date at which each data partner
 will be ready to receive the Diagnostic Query (DQ), for which the
 requirements are:

 • CDM v3.0 with SAS data types
 • All 15 tables present
 • Demographic, Enrollment, Encounter, Diagnosis, Procedures, Vital, and
 Harvest tables populated

 ||Site  ||SAS CDM v3 Readiness Date/DQ Status
 ||Children's Mercy  ||06/15/16
 ||Indiana U Regenstrief ||03/01/16
 ||Marshfield Clinic ||Completed DQ
 ||Med Coll Wisconsin||03/31/16
 ||U of Minnesota AHC||03/31/16
 ||U of Missouri HC  ||06/30/16
 ||U of Nebraska ||3/15/16
 ||University of Iowa||TBD
 ||University of Kansas  ||~~DQ sent 2/2/16~~ March 16
 ||UT San Antonio||DQ sent 2/2/16
 ||UT SW Med Ctr ||DQ sent 2/2/16
 ||UW Madison||03/14/16



 Additionally, please keep the following points in mind for future
 planning:
 1. We will send the Diagnostic Query based on the dates you provide (I
 will check-in the week prior to sending to verify readiness)
 2. We will request a response in ~2 weeks
 3. Requirements for the next step, Data Characterization, are:
 • Successful diagnostic response, ie. no exceptions noted (in the workplan
 they are described as “unexpected conditions”)
 • Locked/static data
 • Will need to submit an ETL ADD with their query response (the template
 is on our Data Characterization wiki)

--

Comment:

 Looks like the next step is for UTHSCSA to fix some things and re-run by
 Feb 16 (comment:8).

 I suppose given the negative result from KUMC (#476) we owe an update ETA.
 Our internal schedule says March 16.

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Re: [gpc-informatics] #473: PCORnet CDMv3 SAS Readiness

[GPC Informatics]

#473: PCORnet CDMv3 SAS Readiness
---+
 Reporter:  lv |   Owner:  lv
 Type:  task   |  Status:  assigned
 Priority:  major  |   Milestone:  gpc-phase2-h1
Component:  data-stds  |  Resolution:
 Keywords: |  Blocked By:
 Blocking: |
---+

Comment (by dconnolly):

 I wondered what "with SAS data types" meant; I see a `SAS_DATA_TYPE`
 column in the data dictionary:
   - [http://www.pcornet.org/wp-content/uploads/2015/06/2015-06-01-PCORnet-
 Common-Data-Model-v3dot0-parseable.xlsx 2015-06-01 PCORnet Common Data
 Model v3.0 – parseable]
 - linked from [http://www.pcornet.org/pcornet-common-data-model/
 PCORnet Common Data Model (CDM) - PCORnet]

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Re: [gpc-informatics] #266: CDM V3 Development for Phase 2

[GPC Informatics]

#266: CDM V3 Development for Phase 2
--+---
 Reporter:  campbell  |   Owner:  lv
 Type:  design-issue  |  Status:  closed
 Priority:  major |   Milestone:  bariatric-study-data
Component:  data-stds |  Resolution:  duplicate
 Keywords:  CDM V3|  Blocked By:  381, 436
 Blocking:|
--+---
Changes (by dconnolly):

 * status:  accepted => closed
 * resolution:   => duplicate
 * blockedby:  283, 381, 436 => 381, 436


Comment:

 As far as I can tell, this isn't interestingly different from #473.

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GPC Feasibility Query: Effects of Medicaid Expansion on Cancer Care in the United States

[Tamara McMahon]

All,

The GPC received a feasibility request that includes a questionnaire and 
multiple queries from Dr. Laura Tenner at UTHSC-SA.  Queries are located on 
Babel at Shared\Medicaid Expansion  Alex Bokov is a contact for questions 
regarding these queries.

Submit the attached spreadsheet with counts and the informatics questionnaire 
via this survey.

This request has a short turnaround.  Counts are due Monday 2/22.  CMH is not 
required to submit counts as this is geared toward an adult population.

This request is currently under DROC review.  The following institutions have 
DROC approval and can submit their site counts and survey at any time.

KUMC
Iowa
MCW
Marshfield
UTHSC-SA
Missouri

The following sites do not have DROC approval yet.  You can work on the counts 
but please do not submit until approval is in place for your institution.

Wisconsin
Minnesota
Nebraska
UTSW
Indiana

We can discuss any questions regarding this request at the GPC-Dev call 
tomorrow.

Regards,
Tamara McMahon
Director, Engineering and Product Experience
Division of Medical Informatics
University of Kansas Medical Center
913-945-7470



ACA_site_team_questionnaire.doc
Description: ACA_site_team_questionnaire.doc


ACA_cancer_prepquery.xls
Description: ACA_cancer_prepquery.xls
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RE: Gather 2015 4th quarterly QA results

[Green, Timothy A.]

The patient demographics are stored in our i2b2 in the person dimension.  The 
QA scripts are written with the assumption that all data is stored in the fact 
table.  There is no provision for the script to leverage the ontology 
architecture to determine the storage location of the various pieces of data.  
I'm sure it was done that way to simplify the script, but it does ignore a 
pretty major feature of i2b2: the ontology mapping functionality.  This makes 
it less portable to sites that have a different implementation of the ontology. 
 I don't characterize a difference in implementation a problem in the data 
warehouse.

Keep in mind that MU had an i2b2 instance back in 2014, and the MU architecture 
was established before joining the GPC.  It would be work to either shift our 
demographics storage (and additional storage capacity), or to rewrite the QA 
scripts.  We will opt to rewrite the QA scripts, but to do it in a portable way 
(i.e. we could share our changes back to the GPC) will require some complexity 
of coding to leverage the ontology framework in i2b2.  We may have to opt for 
hardcoding our version against the dimension table.

Aside from that, we still have the relatively simple task of mapping our 
concept codes/paths to get the remainder (non-demographic part) of the script 
to work correctly.

Tim



From: Mosa, Abu S.
Sent: Monday, February 15, 2016 10:20 AM
To: Dan Connolly
Cc: ; Green, Timothy A.; McNeeley, Todd A.
Subject: RE: Gather 2015 4th quarterly QA results

I would defer this to Tim and Todd to share their thoughts on this. Thanks. 
--Mosa

From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 10:03 AM
To: Mosa, Abu S. mailto:mo...@health.missouri.edu>>
Cc: mailto:gpc-dev@listserv.kumc.edu>> 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: RE: Gather 2015 4th quarterly QA results

What are the symptoms when you try to run the QA scripts, Mosa? What 
diagnostics do you get?

The premise of the QA scripts is that if they don't run, that's a problem with 
your data warehouse. Perhaps there are actually problems with the scripts, but 
if so, we need details on what those problems are. Also, we have a shared 
source code repository in 
gpc-qa-quarterly. So if you 
make changes, please strive to make them portable to other sites.

p.s. I presume it's OK to share this thread with gpc-dev, as it regards group 
technical work.

--
Dan

From: Mosa, Abu S. [mo...@health.missouri.edu]
Sent: Friday, February 12, 2016 4:41 PM
To: Dan Connolly
Subject: Gather 2015 4th quarterly QA results
Hi Dan,

I talked with our technical team about generating the 2015 4th quarterly 
report. They looked into the MSSQL code that you referred to me on BitBucket. 
They advised that major re-writing effort is needed in order to localize the 
scripts to be able to run on our i2b2 data model. They are currently focusing 
on the Phase I implementation (specifically tumor registry data load) which 
they target to complete by end of this month. So, a viable timeline for 
generating the 2015 4th quarterly report for us would be Mid-march. Let me know 
if you have any questions. If needed, we can discuss this during the next Dev 
call.

Regards,
Abu Saleh Mohammad Mosa, PhD
Director, Research Informatics
Institute for Clinical and Translational Science
University of Missouri


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RE: Gather 2015 4th quarterly QA results

[Mosa, Abu S.]

I would defer this to Tim and Todd to share their thoughts on this. Thanks. 
--Mosa

From: Dan Connolly [mailto:dconno...@kumc.edu]
Sent: Monday, February 15, 2016 10:03 AM
To: Mosa, Abu S. 
Cc:  
Subject: RE: Gather 2015 4th quarterly QA results

What are the symptoms when you try to run the QA scripts, Mosa? What 
diagnostics do you get?

The premise of the QA scripts is that if they don't run, that's a problem with 
your data warehouse. Perhaps there are actually problems with the scripts, but 
if so, we need details on what those problems are. Also, we have a shared 
source code repository in 
gpc-qa-quarterly. So if you 
make changes, please strive to make them portable to other sites.

p.s. I presume it's OK to share this thread with gpc-dev, as it regards group 
technical work.

--
Dan

From: Mosa, Abu S. [mo...@health.missouri.edu]
Sent: Friday, February 12, 2016 4:41 PM
To: Dan Connolly
Subject: Gather 2015 4th quarterly QA results
Hi Dan,

I talked with our technical team about generating the 2015 4th quarterly 
report. They looked into the MSSQL code that you referred to me on BitBucket. 
They advised that major re-writing effort is needed in order to localize the 
scripts to be able to run on our i2b2 data model. They are currently focusing 
on the Phase I implementation (specifically tumor registry data load) which 
they target to complete by end of this month. So, a viable timeline for 
generating the 2015 4th quarterly report for us would be Mid-march. Let me know 
if you have any questions. If needed, we can discuss this during the next Dev 
call.

Regards,
Abu Saleh Mohammad Mosa, PhD
Director, Research Informatics
Institute for Clinical and Translational Science
University of Missouri


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Re: [gpc-informatics] #327: Gather 2015 4th quarterly QA results (and 3rd quarter if feasible)

[GPC Informatics]

#327: Gather 2015 4th quarterly QA results (and 3rd quarter if feasible)
-+-
 Reporter:  mish |   Owner:  mish
 Type:  problem  |  Status:  assigned
 Priority:  major|   Milestone:  data-quality-q3
Component:  data-|  Resolution:
  quality|  Blocked By:  290, 309, 326, 351, 366, 392, 439,
 Keywords:   |  450
 Blocking:   |
-+-

Comment (by rfothergill):

 CMH has uploaded Q4 results

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Agenda items 2015-02-15

[Tamara McMahon]

The GPC received a feasibility query request with a short turnaround time (due 
2/22).  It is currently in DROC review.  I would like to add the following to 
the 2/16 DEV agenda.

Feasibility Query: Effects of Medicaid Expansion on Cancer Care in the United 
States

-  Discuss queries

-  Informatics questionnaire

-  When/where sites can submit the counts

I can update the agenda with a pointer to the honest broker email once I send 
it later today.

Tamara McMahon
Director, Engineering and Product Experience
Division of Medical Informatics
University of Kansas Medical Center
913-945-7470

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RE: Gather 2015 4th quarterly QA results

[Dan Connolly]

What are the symptoms when you try to run the QA scripts, Mosa? What 
diagnostics do you get?

The premise of the QA scripts is that if they don't run, that's a problem with 
your data warehouse. Perhaps there are actually problems with the scripts, but 
if so, we need details on what those problems are. Also, we have a shared 
source code repository in 
gpc-qa-quarterly. So if you 
make changes, please strive to make them portable to other sites.

p.s. I presume it's OK to share this thread with gpc-dev, as it regards group 
technical work.

--
Dan


From: Mosa, Abu S. [mo...@health.missouri.edu]
Sent: Friday, February 12, 2016 4:41 PM
To: Dan Connolly
Subject: Gather 2015 4th quarterly QA results

Hi Dan,

I talked with our technical team about generating the 2015 4th quarterly 
report. They looked into the MSSQL code that you referred to me on BitBucket. 
They advised that major re-writing effort is needed in order to localize the 
scripts to be able to run on our i2b2 data model. They are currently focusing 
on the Phase I implementation (specifically tumor registry data load) which 
they target to complete by end of this month. So, a viable timeline for 
generating the 2015 4th quarterly report for us would be Mid-march. Let me know 
if you have any questions. If needed, we can discuss this during the next Dev 
call.

Regards,
Abu Saleh Mohammad Mosa, PhD
Director, Research Informatics
Institute for Clinical and Translational Science
University of Missouri


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Re: [gpc-informatics] #327: Gather 2015 4th quarterly QA results (and 3rd quarter if feasible)

[GPC Informatics]

#327: Gather 2015 4th quarterly QA results (and 3rd quarter if feasible)
-+-
 Reporter:  mish |   Owner:  mish
 Type:  problem  |  Status:  assigned
 Priority:  major|   Milestone:  data-quality-q3
Component:  data-|  Resolution:
  quality|  Blocked By:  290, 309, 326, 351, 366, 392, 439,
 Keywords:   |  450
 Blocking:   |
-+-

Comment (by dconnolly):

 Not seeing any news, I moved the due date for milestone:data-quality-q3
 from Feb 15 to Feb 29.

 The relevance to Q4 2015 is fading; we probably should have started on Q1
 2016 by now.

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Re: scribe for gpc-dev tomorrow?

[Taylor, Bradley]

George from MCW will do it.

From: 
mailto:gpc-dev-boun...@listserv.kumc.edu>> 
on behalf of Dan Connolly mailto:dconno...@kumc.edu>>
Date: Monday, February 15, 2016 at 9:45 AM
To: "mailto:gpc-dev@listserv.kumc.edu>>" 
mailto:gpc-dev@listserv.kumc.edu>>
Subject: scribe for gpc-dev tomorrow?

Jay at UNMC wants to get a little better oriented before he serves as scribe, 
so I am recruiting a different scribe for tomorrow. Volunteers?

--
Dan

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scribe for gpc-dev tomorrow?

[Dan Connolly]

Jay at UNMC wants to get a little better oriented before he serves as scribe, 
so I am recruiting a different scribe for tomorrow. Volunteers?

--
Dan

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Re: [gpc-informatics] #273: ADAPTABLE study ID linkage, REDCap integration

[Tyrus Rorick]

This is not yet available - our focus has been on the patient facing part of 
the portal.  We should be able to provide an update on what we can provide and 
when in the next week.  Stay tuned…
Best, Ty




On 2/12/16, 3:01 PM, "Sravani Chandaka"  wrote:

>Copying Tyrus Rorick.
>
>On 2/12/16, 1:55 PM, "Russ Waitman"  wrote:
>
>>Hi Shelley,
>>While it may not be "live", is there a test file specification for the
>>tickets and the download of the Mytrus reports so we can communicate
>>enrollment back to the sites and physicians?
>>
>>Russ
>>
>>-Original Message-
>>From: GPC Informatics [mailto:d...@madmode.com]
>>Sent: Friday, February 12, 2016 1:26 PM
>>To: Russ Waitman; Sravani Chandaka; Dan Connolly; Nathan Graham
>>Cc: Tamara McMahon; verhagen.lau...@mcrf.mfldclin.edu
>>Subject: Re: [gpc-informatics] #273: ADAPTABLE study ID linkage, REDCap
>>integration
>>
>>#273: ADAPTABLE study ID linkage, REDCap integration
>>-+
>> Reporter:  rwaitman |   Owner:  schandaka
>> Type:  enhancement  |  Status:  assigned
>> Priority:  major|   Milestone:  adaptable-accrual
>>Component:  data-sharing |  Resolution:
>> Keywords:  adaptable-study  |  Blocked By:
>> Blocking:  353  |
>>-+
>>
>>Comment (by schandaka):
>>
>> I got a response from the Duke regarding the golden tickets. Mytrus
>>portal  is not yet available to request the golden tickets.They are very
>>close to  finalizing the portal screen shots, content, and flow ­ once
>>that is  completed they will move to the administrative side of the
>>portal which is  much less intense.  They will keep us posted.
>>
>>--
>>Ticket URL: 
>>
>>gpc-informatics 
>>Greater Plains Network - Informatics
>
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