MCW new NLP Service

[Kowalski, George]

All,

We have a new NLP Service publically available :

https://cis.ctsi.mcw.edu/nlp/

Documentation to follow.

G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu
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Re: Running the PCORNet EDC SAS on Linux

[Kowalski, George]

Ours ran , no issues . Would a copy of the log be useful ? I can send it to you 
via your securefiles.ku.edu web site.

G


From: Gpc-dev  on behalf of Michael Prittie 

Date: Wednesday, June 21, 2017 at 9:03 AM
To: "gpc-dev@listserv.kumc.edu" 
Subject: Running the PCORNet EDC SAS on Linux

Hi all,
We are trying to move from executing the CDM EDC SAS code on a Windows machine 
to a Linux server here at KUMC.  We have SAS installed on the server, I was 
able to execute a small SAS script which selected from the Oracle CDM tables, 
and was able to run the data step view prep and inspect code successfully.  
Unfortunately though, when I run the v3.1 Beta EDC it falls over with errors 
early on in DEM_L3_GENDERDIST.  Comparing the log files located in the drnoc 
directory on both the failed Linux run and a successful Windows run I found 
that only the Linux run contains the following set of errors (repeatedly):

ERROR: Variable _FREQ_ is not on file WORK.STATS.
ERROR: Invalid DROP, KEEP, or RENAME option on file WORK.STATS.
ERROR: Variable _type_ is not on file WORK.STATS.

While it’s obvious that the problem has something to do with the WORK.STATS 
dataset, I haven’t had any luck diagnosing what that problem is exactly, or why 
it would occur on our linux box, but not our Windows one.  If anyone has any 
experience with or insights about this problem any leads would be much 
appreciated.

Thanks,

Michael Prittie
Biomedical Informatics Software Engineer
Division of Medical Informatics
University of Kansas Medical Center
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Re: help moving CDM SAS to linux

[Kowalski, George]

Dan,

We run sas on linux and have not seen it on any queries, but we’re not running 
the new CDM Beta code . If we can get the new i2p_transform code to connect to 
Oracle , We’re chomping at the bit to try this out .

G



From: Gpc-dev  on behalf of Dan Connolly 

Date: Friday, June 2, 2017 at 8:49 AM
To: "gpc-dev@listserv.kumc.edu" 
Subject: help moving CDM SAS to linux

We're hitting these errors only on linux; anybody seen them?


1965: ERROR: Variable _FREQ_ is not on file WORK.STATS.

1966: ERROR: Invalid DROP, KEEP, or RENAME option on file WORK.STATS.

1967: ERROR: Variable _type_ is not on file WORK.STATS.

...


--
Dan

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combining notes

[Kowalski, George]

All ,

Per yesterday’s call:  Not much to the code to combine text notes . Our main 
query is :

SELECT
pm.date_off,
hnt.*
FROM
hno_note_text hnt
LEFT OUTER JOIN
patient_mapping pm
ON
hnt.pat_id = pm.pat_id
WHERE
hnt.note_id IS NOT NULL
AND hnt.pat_id IS NOT NULL
ORDER BY
hnt.note_id,
hnt.note_csn_id,
hnt.line

we join to patient_mapping as that contains the date offset we store per user 
for shifting dates.

With this result set we iterate over the results and concatenate that rows text 
if the CSN ID of that row matches the last row. Then write it to a matching 
table (except it has an extra column for the date_offset and an empty column 
for de-identified notes that we generate later )  The only trick we found is 
that when combining rows of text , we had to place a space between each row or 
we generated  concatenated words.

G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu
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Re: Linking Geocoding data with i2b2

[Kowalski, George]

Phil,

I just created the table  in oracle  , shooting from the hip :

CREATE TABLE
MCW_GEOCODING
(
OID INTEGER,
JOIN_COUNT INTEGER,
TARGET_FID INTEGER,
LOC_NAME VARCHAR2(200),
STATUS VARCHAR2(200),
SCORE INTEGER,
MATCH_TYPE VARCHAR2(200),
X FLOAT(126),
Y FLOAT(126),
MATCH_ADDR VARCHAR2(200),
DISP_LON VARCHAR2(200),
DISP_LAT VARCHAR2(200),
SIDE VARCHAR2(200),
ARC_ADDRESS VARCHAR2(200),
ARC_CITY VARCHAR2(200),
ARC_STATE VARCHAR2(200),
ARC_ZIP VARCHAR2(200),
ADDRESS VARCHAR2(200),
CITY VARCHAR2(200),
STATE VARCHAR2(200),
ZIP VARCHAR2(200),
NEW_X FLOAT(126),
NEW_Y FLOAT(126),
ID VARCHAR2(200),
BLOCK_ID VARCHAR2(200),
FIPSST VARCHAR2(200),
FIPSCO VARCHAR2(200),
FIPSSTCO VARCHAR2(200),
TRACT_ID VARCHAR2(200),
ST_ABRV VARCHAR2(200),
CO_NAME VARCHAR2(200),
ST_NAME VARCHAR2(200)
);

Used dbvisulizer to import the data directly into this table.



From: Gpc-dev  on behalf of Phillip Reeder 

Date: Wednesday, May 24, 2017 at 1:10 PM
To: "gpc-dev@listserv.kumc.edu" 
Subject: Linking Geocoding data with i2b2

#1) Now that we have the geocoding data, is there a document somewhere that 
summarizes what the next steps are?  For example, which census files should we 
load?  Is there a standard process for loading that data into Oracle? Any 
helpful tips for working with the data?

#2) Has there been any additional work done with integrating i2b2 and the 
geocoding data?  The last I see is from almost a year ago.  Would it be 
possible to get a short presentation of the current state of that process?  
There are several people in my group that would like to see what that looks 
like.

Thanks,
Phillip



UT Southwestern


Medical Center



The future of medicine, today.


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question on GROUSE Extract

[Kowalski, George]

All,

Per todays call referencing ticket 
(https://informatics.gpcnetwork.org/trac/Project/ticket/595 ), we've had 
further discussion here at MCW and have a question.

Is this extract only for Grouse at this time or is this going to be also be 
used for the "Cancer CRG" with this initial pull?

We have had previous communications with Betsy,  and conveyed to her that our 
data is currently missing the Meds Admin data required for chemo dosing . 
Getting this data into our I2B2 instance is 2 months out. If this is not a 
requirement now, we can dump the requested files and upload them to KU. But if 
the expectation is that this data will be usable now for the Cancer CRG, we 
suggest that we hold off until we get that data loaded.?

George

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the Encounter Types for Insurance Coverage

[Kowalski, George]

All,

Per todays GPC Call : Here ( at MCW ) are the Encounter Types we determined 
were to be included when looking for Insurance Coverage

ENC_TYPE_C

NAME

99

Billing Encounter

1000

Cardiology Consult Visit

500526

Cardiology Nurse Only Visit

500522

Cardiology Office Visit

223

Cardiology Procedure

218

Clinic Assistant

156

Diagnostic Lab

62

E-Visit

500542

Endo NH (North Hills) Procedure

5003049

Equipment Dispense Visit

500518

Evaluation

500528

GI Nurse Only Visit

500527

GI Office Visit

92

Home Care Update

91

Home Care Visit

154

Home Health

85

Hospice Admission

3

Hospital Encounter

210

Lab Only

49

Lactation Encounter

50063

MyChart Video Visit

200

Nurse Only

213

Nutrition

500541

OB CLINIC ASSIST

500537

OB Nurse Only

500514

OB Office Visit

101

Office Visit

160

Office Visit W/O Level of Service (LOS)

500544

Ortho Office Visit

500547

Plastics and Hand Clinic

1003

Procedure Visit

500525

Remote Device Check

5001128

Sleep Center Procedure

5011128

Sleep Center Visit

500516

Social Services

211

Social Work

500529

Team Conferences

76

Telemedicine

500515

Therapy

500531

Transplant Nurse Only

500530

Transplant Office Visit

50062

Video-Visit




George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu
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FW: Med Coll Wisconsin's r003 approved

[Kowalski, George]

We’ve been approved.

From: "Kowalski, George" <gkowal...@mcw.edu>
Date: Monday, April 24, 2017 at 8:44 AM
To: CRDW <c...@mcw.edu>
Subject: FW: Med Coll Wisconsin's r003 approved



From: PCORnet DRN OC <dr...@pcornet.org>
Date: Monday, April 24, 2017 at 8:43 AM
To: "Osinski, Kristen" <kosin...@mcw.edu>, "Kowalski, George" 
<gkowal...@mcw.edu>, LAUREL VERHAGEN <verhagen.lau...@mcrf.mfldclin.edu>, 
"greenlee.robert" <greenlee.rob...@mcrf.mfldclin.edu>, Russ Waitman 
<rwait...@kumc.edu>
Cc: Laura Qualls <laura.qua...@duke.edu>, "Darcy Louzao, Ph.D." 
<darcy.lou...@duke.edu>, James Topping <james.topp...@duke.edu>
Subject: Med Coll Wisconsin's r003 approved

Good morning.

I’m happy to report that C4MCW's data characterization query response for 
refresh 3 was approved.   Please retain a static, locked copy of the SAS 
version of the characterized tables and use these data when responding to SAS 
queries issued by the DRN OC or study teams, unless instructed otherwise.  You 
may update the SAS version of all non-characterized tables and your RDBMS 
DataMart as needed.  Please contact the DRN OC if an off-cycle refresh is 
required for any of following tables: DEMOGRAPHIC, DEATH, DIAGNOSIS, 
DISPENSING, ENROLLMENT, ENCOUNTER, LAB_RESULT_CM, PRESCRIBING, PROCEDURES, and 
VITAL.

Thanks,
DRN OC Data Characterization Team
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Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

[Kowalski, George]

Well just some testing after I cleaned out our data.

Logged back into babel and started clicking on ontologies. First one I tried 
“CMH: Diagnosis” thru a “Database Error” also. But  “CMH: Demographics” worked.

Weird but all our ontologies are still there at the top level and still throw 
“Database Error”  when I expand them.


G


From: Gpc-dev <gpc-dev-boun...@listserv.kumc.edu> on behalf of "Kowalski, 
George" <gkowal...@mcw.edu>
Date: Wednesday, April 12, 2017 at 8:04 AM
To: "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

I’ve emptied our terms table until such time as we can determine what’s going 
wrong with the import process.



From: Gpc-dev 
<gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>> 
on behalf of "Kowalski, George" <gkowal...@mcw.edu<mailto:gkowal...@mcw.edu>>

Date: Wednesday, April 12, 2017 at 8:00 AM

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

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



All,







I reloaded our ontology here at MCW on Monday , It seemed to go well via 
phpPgAdmin, but Now I can’t browse our ontology without a “database error”  
coming back .











From: Gpc-dev 
<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%3e>>
 on behalf of "Klann, Jeffrey G." 
<jeff.kl...@mgh.harvard.edu<mailto:jeff.kl...@mgh.harvard.edu><mailto:jeff.kl...@mgh.harvard.edu><mailto:jeff.kl...@mgh.harvard.edu%3e>>



Date: Tuesday, April 11, 2017 at 10:37 PM



To: 
"gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu><mailto:gpc-dev@listserv.kumc.edu><mailto:gpc-dev@listserv.kumc.edu%3e>"
 
<gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu><mailto:gpc-dev@listserv.kumc.edu><mailto:gpc-dev@listserv.kumc.edu%3e>>,
 
"jay.peder...@unmc.edu<mailto:jay.peder...@unmc.edu><mailto:jay.peder...@unmc.edu><mailto:jay.peder...@unmc.edu%3e>"
 
<jay.peder...@unmc.edu<mailto:jay.peder...@unmc.edu><mailto:jay.peder...@unmc.edu><mailto:jay.peder...@unmc.edu%3e>>,
 
"campb...@unmc.edu<mailto:campb...@unmc.edu><mailto:campb...@unmc.edu><mailto:campb...@unmc.edu%3e>"
 
<campb...@unmc.edu<mailto:campb...@unmc.edu><mailto:campb...@unmc.edu><mailto:campb...@unmc.edu%3e>>,
 
"huhick...@nebraskamed.com<mailto:huhick...@nebraskamed.com><mailto:huhick...@nebraskamed.com><mailto:huhick...@nebraskamed.com%3e>"
 
<huhick...@nebraskamed.com<mailto:huhick...@nebraskamed.com><mailto:huhick...@nebraskamed.com><mailto:huhick...@nebraskamed.com%3e>>,
 
"dconno...@kumc.edu<mailto:dconno...@kumc.edu><mailto:dconno...@kumc.edu><mailto:dconno...@kumc.edu%3e>"
 
<dconno...@kumc.edu<mailto:dconno...@kumc.edu><mailto:dconno...@kumc.edu><mailto:dconno...@kumc.edu%3e>>,
 
"rwait...@kumc.edu<mailto:rwait...@kumc.edu><mailto:rwait...@kumc.edu><mailto:rwait...@kumc.edu%3e>"
 
<rwait...@kumc.edu<mailto:rwait...@kumc.edu><mailto:rwait...@kumc.edu><mailto:rwait...@kumc.edu%3e>>



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







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















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















Thanks,















Jeffrey Klann, PhD







Instructor of Medicine, Harvard Medical School







Instructor in Investigation, Massachusetts General Hospital























On 4/11/17, 12:00 PM, "GPC Informatics" 
<d...@madmode.com<mailto:d...@madmode.com><mailto:d...@madmode.com><mailto:d...@madmode.com><mailto:d...@madmode.com%3e><mailto:d...@madmode.com%3e%3cmailto:d...@madmode.com%3e%3cmailto:d...@madmode.com%3e%3e>>
 wrote:















#280: Medication ontology orgainzed by ingredient







-+







 Reporter:  preeder  |   Owner:  jay.pedersen







 Type:  enhancement  |  Status:  assigned







 Priority:  major|   Milestone:  snow-shrine-2







Component:  data-stds|  Resolution:







 Keywords:   |  Blocked By:







 Blocking:   |







-

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

[Kowalski, George]

I’ve emptied our terms table until such time as we can determine what’s going 
wrong with the import process.

From: Gpc-dev <gpc-dev-boun...@listserv.kumc.edu> on behalf of "Kowalski, 
George" <gkowal...@mcw.edu>
Date: Wednesday, April 12, 2017 at 8:00 AM
To: "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

All,



I reloaded our ontology here at MCW on Monday , It seemed to go well via 
phpPgAdmin, but Now I can’t browse our ontology without a “database error”  
coming back .





From: Gpc-dev 
<gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>> 
on behalf of "Klann, Jeffrey G." 
<jeff.kl...@mgh.harvard.edu<mailto:jeff.kl...@mgh.harvard.edu>>

Date: Tuesday, April 11, 2017 at 10:37 PM

To: "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" 
<gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>>, 
"jay.peder...@unmc.edu<mailto:jay.peder...@unmc.edu>" 
<jay.peder...@unmc.edu<mailto:jay.peder...@unmc.edu>>, 
"campb...@unmc.edu<mailto:campb...@unmc.edu>" 
<campb...@unmc.edu<mailto:campb...@unmc.edu>>, 
"huhick...@nebraskamed.com<mailto:huhick...@nebraskamed.com>" 
<huhick...@nebraskamed.com<mailto:huhick...@nebraskamed.com>>, 
"dconno...@kumc.edu<mailto:dconno...@kumc.edu>" 
<dconno...@kumc.edu<mailto:dconno...@kumc.edu>>, 
"rwait...@kumc.edu<mailto:rwait...@kumc.edu>" 
<rwait...@kumc.edu<mailto:rwait...@kumc.edu>>

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



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







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







Thanks,







Jeffrey Klann, PhD



Instructor of Medicine, Harvard Medical School



Instructor in Investigation, Massachusetts General Hospital











On 4/11/17, 12:00 PM, "GPC Informatics" 
<d...@madmode.com<mailto:d...@madmode.com><mailto:d...@madmode.com><mailto:d...@madmode.com%3e>>
 wrote:







#280: Medication ontology orgainzed by ingredient



-+



 Reporter:  preeder  |   Owner:  jay.pedersen



 Type:  enhancement  |  Status:  assigned



 Priority:  major|   Milestone:  snow-shrine-2



Component:  data-stds|  Resolution:



 Keywords:   |  Blocked By:



 Blocking:   |



-+







Comment (by dconnolly):







 Replying to [comment:19 campbell]:



 > SCILHS/Medication metadata issues addressed with load to BABEL toiday:







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



 Medications (UNMC)**?







 > • (therefore) with VA drug classes as sole top-level ontology, not



 all clinical formulations or packages can be deployed







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







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







--



Ticket URL: 
<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_trac_Project_ticket_280-23comment-3A20=DwIGaQ=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y=C_iDrPTjMjNVakiaVcSiVk-6jAlbEoLBTtmMo_3OTb0=OweRWiaUZzSbQdgaQuxsxHqDK80FJf9Laofx0ZRAuRw=Gamomccl8eONNAqA0xxXdwPZxPo_We-msfkKsS1zAc0=>



gpc-informatics 
<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_=DwIGaQ=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y=C_iDrPTjMjNVakiaVcSiVk-6jAlbEoLBTtmMo_3OTb0=OweRWiaUZzSbQdgaQuxsxHqDK80FJf9Laofx0ZRAuRw=lDqm9XxOCpZnAuPAyrKhcoBHWFiMMCtQ6GrEkXYmQgM=>



Greater Plains Network - Informatics















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Re: about the Babel problem

[Kowalski, George]

So what’s file file size limit now ?


From: Gpc-dev  on behalf of Debbie Yoshihara 

Date: Monday, April 10, 2017 at 9:38 AM
To: Nathan Graham , Lav Patel 
Cc: gpc-dev 
Subject: Re: about the Babel problem


Worked with Nathan and Lav to increase the php.ini file on Babel and now I was 
able to import the ontology tables to Babel as usual.



--- Debbie


From: Debbie Yoshihara
Sent: Monday, April 10, 2017 9:31:42 AM
To: Nathan Graham
Cc: Lav Patel
Subject: Re: about the Babel problem


Nathan,



That did it!  I was able to import the biggest file DIAGNOSIS.

I'm still in the process of importing the others.

Thanks!



-- Debbie


From: Nathan Graham 
Sent: Monday, April 10, 2017 9:02:28 AM
To: Debbie Yoshihara
Cc: Lav Patel
Subject: RE: about the Babel problem

Debbie,

Lav found that the PHP values were indeed set to a much lower value than on the 
old Babel.  We’ve now upped the values and restarted services – would you be 
willing to try again?

--
Nathan

From: Nathan Graham
Sent: Monday, April 10, 2017 8:44 AM
To: 'Debbie Yoshihara'
Cc: Lav Patel
Subject: RE: about the Babel problem

Ok, thanks for your help – we’ll double check the configuration and let you 
know.

From: Debbie Yoshihara [mailto:dlyos...@wisc.edu]
Sent: Monday, April 10, 2017 8:42 AM
To: Nathan Graham
Cc: Lav Patel
Subject: Re: about the Babel problem


https://babel.gpcnetwork.org/db-ide



and I use import.  The small file uploaded, the bigger files got the error 
message

Server not found or something like that.



--- Debbie


From: Nathan Graham >
Sent: Monday, April 10, 2017 8:39:54 AM
To: Debbie Yoshihara
Cc: Lav Patel
Subject: RE: about the Babel problem

That’s a good idea – which babel interface are you using (URL)?  We tried 
several different methods – Jay was trying to use SSH and we don’t have the 
ports open for that yet so we know what’s wrong there.

I think one of the web interfaces is phpPgAdmin so if you’re using that you 
might be right – we can up the upload limit and let you try again.

--
Nathan

From: Debbie Yoshihara [mailto:dlyos...@wisc.edu]
Sent: Monday, April 10, 2017 8:35 AM
To: Nathan Graham
Subject: about the Babel problem
Importance: High


Nathan,



Could you check the php.ini file and see what the maximum size is allowed?

The Babel server seems to be new and maybe the php.ini file is not tuned 
correctly.

Babel uploads were working for me as of Feb 2017, but now only tiny files are 
let through.



--- Debbie
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Re: [Gpc-deid] Agenda for todays webex meeting

[Kowalski, George]

Laurel / All ,

Ah yes there seems to have been  a problem with the email list , it is now 
sending all the queued up emails that we’ve sent over the last few days.

So we had our first webex meeting this last Tuesday.  Notes are here :

https://wiki.ctri.mcw.edu/display/GDD/April+2017+Meeting

We didn’t talk much about how to address the issues your team brought up as we 
had bigger outstanding issues to address in our first call. If anyone wants an 
invite to these monthly calls ( first Tuesday of the month at 11am CST ) I can 
add you . Just drop me an email directly.

G




From: LAUREL VERHAGEN <verhagen.lau...@mcrf.mfldclin.edu>
Date: Friday, April 7, 2017 at 11:20 AM
To: "Kowalski, George" <gkowal...@mcw.edu>
Subject: RE: [Gpc-deid] Agenda for todays webex meeting

Hi George,

What meeting? When?

Thanks,
Laurel

-Original Message-
From: Gpc-deid [mailto:gpc-deid-boun...@listserv.kumc.edu] On Behalf Of 
Kowalski, George
Sent: Thursday, April 06, 2017 10:39 AM
To: gpc-d...@listserv.kumc.edu<mailto:gpc-d...@listserv.kumc.edu>
Subject: [Gpc-deid] Agenda for todays webex meeting

All,
I have the following for todays meeting :

https://urldefense.proofpoint.com/v2/url?u=https-3A__wiki.ctri.mcw.edu_display_GDD_April-2B2017-2BMeeting=DwICAg=KNVzINr6WAqWApikNSnyDeOu0ck0iFwcrMz92MxUhIs=A2PXk2ZGVGBzoEOQMwrrbqse0CnDMUgS4P3-3HOTSAwE8Vfvoc1Wm0NCYFbuU-_5=oCqf__bmNLdCdxGUeqll9m9zO5tIBz94nvflDz1B_h4=yP-MDaLq9sRRr0KZTyu6TbPqBqQobYhWYFjgfYVENws=

Let me know if there is other stuff to talk about .

G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu<mailto:gkowal...@mcw.edu><mailto:gkowal...@mcw.edu>
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Re: MCW Shrine demographics online

[Kowalski, George]

Yes , per your email , that’s the SHRINE Ontology I’ve loaded and the one I’m 
mapping to  .

http://imgur.com/a/h1qza


G


From: Phillip Reeder <phillip.ree...@utsouthwestern.edu>
Date: Monday, April 3, 2017 at 5:08 PM
To: "Kowalski, George" <gkowal...@mcw.edu>
Cc: "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>
Subject: Re: MCW Shrine demographics online

Have you started looking at the SCIHLS PCORI terminologies I sent out a couple 
weeks ago?  Any progress on moving to that terminology?

Phillip

Sent from my iPhone

On Apr 3, 2017, at 5:05 PM, Kowalski, George 
<gkowal...@mcw.edu<mailto:gkowal...@mcw.edu>> wrote:

All,

I’ve mapped the SHRINE demographics concepts from our ontology to the SCHILS 
ontology in case anyone wants to test against our server. It’s pointing to our 
production I2B2 instance so you will get back real numbers.  I still get errors 
from all the other sites  for any of the demographic terms, but Keith said that 
was to be expected for now.

WISC SPOKE PRD "Hispani-Female@16:48:08"
- Could not map query term(s).<https://snow.ctri.mcw.edu:6443/shrine-webclient/>

WISC SPOKE DEV "Hispani-Female@16:48:08"
- Could not map query term(s).<https://snow.ctri.mcw.edu:6443/shrine-webclient/>

KUMC SPOKE TEST "Hispani-Female@16:48:08"
- Could not map query term(s).<https://snow.ctri.mcw.edu:6443/shrine-webclient/>

marshfield "Hispani-Female@16:48:08"
- Could not map query term(s).<https://snow.ctri.mcw.edu:6443/shrine-webclient/>

UT Southwestern "Hispani-Female@16:48:08"
- Could not map query term(s).<https://snow.ctri.mcw.edu:6443/shrine-webclient/>

IU SPOKE PRD "Hispani-Female@16:48:08"
- An unanticipated problem 
encountered.<https://snow.ctri.mcw.edu:6443/shrine-webclient/>


G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu<mailto:gkowal...@mcw.edu><mailto:gkowal...@mcw.edu>
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UT Southwestern


Medical Center



The future of medicine, today.



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MCW Shrine demographics online

[Kowalski, George]

All,

I’ve mapped the SHRINE demographics concepts from our ontology to the SCHILS 
ontology in case anyone wants to test against our server. It’s pointing to our 
production I2B2 instance so you will get back real numbers.  I still get errors 
from all the other sites  for any of the demographic terms, but Keith said that 
was to be expected for now.

WISC SPOKE PRD "Hispani-Female@16:48:08"
 - Could not map query 
term(s).

WISC SPOKE DEV "Hispani-Female@16:48:08"
 - Could not map query 
term(s).

KUMC SPOKE TEST "Hispani-Female@16:48:08"
 - Could not map query 
term(s).

marshfield "Hispani-Female@16:48:08"
 - Could not map query 
term(s).

UT Southwestern "Hispani-Female@16:48:08"
 - Could not map query 
term(s).

IU SPOKE PRD "Hispani-Female@16:48:08"
 - An unanticipated problem 
encountered.


G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu
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MCW Shrine is online

[Kowalski, George]

All,

MCW’s shrine is online, upgraded, and talking to the UWM hub  after all the 
help Keith provided us this week. ( Ale Asylum – Hopalicious for you )  We now 
have the task of mapping thru the Concept codes to our Ontologies.

George

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GPC-DEID discussion list started

[Kowalski, George]

FYI ,

There is a new Text Notes De-identification discussion list we’ve started :

http://listserv.kumc.edu/mailman/listinfo/gpc-deid

The purpose of this group is to discuss the technical aspects of the 
De-identification Software that the GPC is using.

Feel free to join if you wish to listen in on the discussion, or better yet, 
take part.

Thanks to KU and Maren for setting this up.

G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu
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Re: re-subscribe me please

[Kowalski, George]

Thanks , got it !



From: Hillary Sandoval <hsando...@kumc.edu>
Date: Tuesday, February 14, 2017 at 10:18 AM
To: "Kowalski, George" <gkowal...@mcw.edu>
Cc: "'Gpc-dev@listserv.kumc.edu'" <Gpc-dev@listserv.kumc.edu>
Subject: RE: re-subscribe me please

Hi George,

I just forwarded the series to you!

Thanks,
Hillary

-Original Message-
From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Kowalski, 
George
Sent: Tuesday, February 14, 2017 10:14 AM
To: gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>
Subject: re-subscribe me please

Can some one please send me the meeting invite  ( the outlook one with the link 
to the meeting ) for the GPC-DEV call ? It fell off my calendar somehow.

Thanks

G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu<mailto:gkowal...@mcw.edu><mailto:kosin...@mcw.edu>
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re-subscribe me please

[Kowalski, George]

Can some one please send me the meeting invite  ( the outlook one with the link 
to the meeting ) for the GPC-DEV call ? It fell off my calendar somehow.

Thanks

G


George Kowalski BS
Biomedical Engineer
Biomedical Informatics
(414) 805-7318 (office)
gkowal...@mcw.edu
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Deid and docker presentation

[Kowalski, George]

Here is my presentation from the GPC-DEV Hackathon :

https://docs.google.com/presentation/d/1PyPSTb9IJnOasKtME2RaZAfJOQ3ju8ODbMSqD5B84NI/edit?usp=sharing


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Re: PCORnet Front Door #3 Parkinson's queries

[Kowalski, George]

Thanks , I poked around in the Datamart client tool but only looked at the 
first datamart , which does not have this setting , the other one does.

G


George Kowalski   - (414) 805-7318

From: Michael Prittie <mprit...@kumc.edu>
Date: Tuesday, January 3, 2017 at 10:48 AM
To: "Kowalski, George" <gkowal...@mcw.edu>, "gpc-dev@listserv.kumc.edu" 
<gpc-dev@listserv.kumc.edu>
Subject: Re: PCORnet Front Door #3 Parkinson's queries

Hi George,
Maren and I here at KUMC just ran several of the five new menu driven
queries without this problem.  If you¹re still running into this issue you
might double check that you are specifying the correct schema name under
Settings -> Network Settings -> DataMart Settings -> Model Settings.

Best,
Michael Prittie


On 12/28/16, 10:08 AM, "Gpc-dev on behalf of Kowalski, George"
<gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu> on 
behalf of gkowal...@mcw.edu<mailto:gkowal...@mcw.edu>> wrote:

All,

FYI : the 5 queries that have come thru  for this study are all hard
coded to the ³cdm² schema , if your using another schema name in your cdm
v3 you¹ll have issues running them . We¹re working with PCORNet to get
this addressed.

G


George Kowalski   - (414) 805-7318
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PCORnet Front Door #3 Parkinson's queries

[Kowalski, George]

All,

FYI : the 5 queries that have come thru  for this study are all hard coded to 
the “cdm” schema , if your using another schema name in your cdm v3 you’ll have 
issues running them . We’re working with PCORNet to get this addressed.

G


George Kowalski   - (414) 805-7318
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Re: UNMC -- BC survey -- issue with rxcui values for importing per-medication into RedCap, rxcui values

[Kowalski, George]

Use Russ’s , We’re seeing him stand up there talking right now.  Is there a 
live feed ?

G


George Kowalski
Biomedical Informatics Software Engineer
Clinical & Translational Science Institute
Medical College of Wisconsin
9200 West Wisconsin Avenue, Suite L722A
Milwaukee, Wisconsin USA 53226
 414.805.7318 (office) / gkowal...@mcw.edu


From:  on behalf of Dan Connolly 

Date: Thursday, October 13, 2016 at 9:13 AM
To: "gpc-dev@listserv.kumc.edu" , "Pedersen, Jay G" 

Subject: RE: UNMC -- BC survey -- issue with rxcui values for importing 
per-medication into RedCap, rxcui values


Hi from the LEC... Forgot my laptop. Bummed that I haven't addressed this issue 
yet.

On Oct 12, 2016 12:54 PM, Dan Connolly  wrote:
I'll look into adding those to the data dictionary.

--
Dan

From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on 
behalf of Pedersen, Jay G [jay.peder...@unmc.edu]
Sent: Wednesday, October 12, 2016 12:03 PM
To: gpc-dev@listserv.kumc.edu
Subject: UNMC -- BC survey -- issue with rxcui values for importing 
per-medication into RedCap, rxcui values
Hi,

Looking for insight into the following problem.  When I try to import my 
per-medication CSV files into RedCap, I get errors relating to the "rxcui" 
values.  Specifically:

378861
847229
847262
897121
1298947

I have these documented to mean (I think I have this right, can double-check as 
needed):

378861 ==>
NPH INSULIN HUMAN RECOMB 100 UNIT/ML SUBCUTANEOUS SUSPENSION

847229 ==>
INSULIN GLARGINE 100 UNIT/ML (3 ML) SUBCUTANEOUS PEN

847262 ==>
INSULIN ASPART 100 UNIT/ML SUBCUTANEOUS PEN


897121 ==>
LIRAGLUTIDE 0.6 MG/0.1 ML (18 MG/3 ML) SUBCUTANEOUS PEN INJECTOR


1298947 ==>

PERTUZUMAB 420 MG/14 ML (30 MG/ML) INTRAVENOUS SOLUTION




Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE  68198-5900
402-559-9487 (office)
402-739-3496 (mobile)

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 
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please delete it and immediately contact the sender.

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Re: [gpc-informatics] #328: Codebook for breast cancer aggregated-response dataset

[Kowalski, George]

Dan,

Access denied to this link.

George Kowalski
Biomedical Informatics Software Engineer
Clinical & Translational Science Institute
Medical College of Wisconsin
9200 West Wisconsin Avenue, Suite L722A
Milwaukee, Wisconsin USA 53226
 414.805.7318 (office) / gkowal...@mcw.edu<mailto:gkowal...@mcw.edu>


From: GPC Informatics <d...@madmode.com>
Reply-To: "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>
Date: Monday, September 26, 2016 at 4:15 PM
To: "dconno...@kumc.edu" <dconno...@kumc.edu>, "Kowalski, George" 
<gkowal...@mcw.edu>, "bradley-mcdow...@uiowa.edu" <bradley-mcdow...@uiowa.edu>, 
"rwait...@kumc.edu" <rwait...@kumc.edu>, "vleona...@kumc.edu" 
<vleona...@kumc.edu>, "tmcma...@kumc.edu" <tmcma...@kumc.edu>
Cc: "e-chrischil...@uiowa.edu" <e-chrischil...@uiowa.edu>
Subject: Re: [gpc-informatics] #328: Codebook for breast cancer 
aggregated-response dataset

#328: Codebook for breast cancer aggregated-response dataset
--+
Reporter:  dconnolly |   Owner:  gkowalski
 Type:  enhancement   |  Status:  closed
Priority:  major |   Milestone:  cohort-char-bc-db
Component:  data-sharing  |  Resolution:  fixed
Keywords:|  Blocked By:  360
Blocking:  295   |
--+

Comment (by dconnolly):

I forgot to mention that REDCap provides a nice codebook view of what I've
done to use this codebook in REDCap:

   -
[https://redcap.gpcnetwork.org/redcap_v6.11.5/Design/data_dictionary_codebook.php?pid=32
Breast Cancer Datamart codebook]

--
Ticket URL: 
<http://informatics.gpcnetwork.org/trac/Project/ticket/328#comment:19>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics

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ALS Survey with EMR data - DE-IDENTIFIED Completed for MCW

[Kowalski, George]

MCW has uploaded it’s records into the “ALS Survey with EMR data - 
DE-IDENTIFIED” redcap survey .

G

George Kowalski
Biomedical Informatics Software Engineer
Clinical & Translational Science Institute
Medical College of Wisconsin
9200 West Wisconsin Avenue, Suite L722A
Milwaukee, Wisconsin USA 53226
 414.805.7318 (office) / gkowal...@mcw.edu

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Re: Data Fulfillment form: please review RE: GPC Dev agenda

[Kowalski, George]

Ahh , I was confused by the “Everybody please take a look”  ☺

George Kowalski
Biomedical Informatics Software Engineer
Clinical & Translational Science Institute
Medical College of Wisconsin
9200 West Wisconsin Avenue, Suite L722A
Milwaukee, Wisconsin USA 53226
 414.805.7318 (office) / gkowal...@mcw.edu


From:  on behalf of Tamara McMahon 

Date: Wednesday, August 24, 2016 at 1:53 PM
To: Dan Connolly , "gpc-dev@listserv.kumc.edu" 

Subject: RE: Data Fulfillment form: please review RE: GPC Dev agenda

I will demo the form in the meeting.  Not everyone has access to the project or 
form.

Tamara

From: Dan Connolly
Sent: Wednesday, August 24, 2016 12:23 PM
To: Tamara McMahon; gpc-dev@listserv.kumc.edu
Subject: Data Fulfillment form: please review RE: GPC Dev agenda

Everybody please take a look and let us know what you think. George, I think 
this might be responsive to some issues you have raised.



--
Dan

From: 
gpc-dev-boun...@listserv.kumc.edu 
[gpc-dev-boun...@listserv.kumc.edu] on behalf of Tamara McMahon 
[tmcma...@kumc.edu]
Sent: Wednesday, August 24, 2016 11:25 AM
To: gpc-dev@listserv.kumc.edu
Subject: GPC Dev agenda
Dan,

Can you add the Data Fulfillment form in the DROC Oversight project to the 
agenda?   It is currently in a draft project.  I would like to get honest 
broker/developer feedback.

https://redcap.gpcnetwork.org/redcap_v6.11.5/ProjectSetup/index.php?pid=61

Thanks,
Tamara McMahon
Director, Engineering & Product Experience
Medical Informatics, University of Kansas Medical Center

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Locked out of DataMart Client

[Kowalski, George]

Anyone know whom to contact  support to unlock my account for the datamart 
client  ?

I tried supp...@popmednet.org

They referred me to h...@pcornet.org . No answer from 
them and we have results to return .

Thanks

G


George Kowalski
Biomedical Informatics Software Engineer
Clinical & Translational Science Institute
Medical College of Wisconsin
9200 West Wisconsin Avenue, Suite L722A
Milwaukee, Wisconsin USA 53226
 414.805.7318 (office) / gkowal...@mcw.edu

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PCORnet Modular Program 1 Request Completed

[Kowalski, George]

From today’s call  :

LV - MCW should have received PMP-1 at the same time as KUMC. Alexander to ask 
George

We ran the query and submitted the requested data back  to PCORI last week.

G


George Kowalski
Biomedical Informatics Software Engineer
Clinical & Translational Science Institute
Medical College of Wisconsin
9200 West Wisconsin Avenue, Suite L722A
Milwaukee, Wisconsin USA 53226
 414.805.7318 (office) / gkowal...@mcw.edu

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Re: gpc-dev 10 May meeting?

[Kowalski, George]

Yes I am .

G

George Kowalski
 414.805.7318 (office) / gkowal...@mcw.edu

From: 
> 
on behalf of Dan Connolly >
Date: Tuesday, May 10, 2016 at 9:42 AM
To: ">" 
>
Subject: RE: gpc-dev 10 May meeting?

Let's get together next week, then. Today's meeting is cancelled.

George, is MCW available to scribe 17 May?

--
Dan


From: Dan Connolly
Sent: Monday, May 09, 2016 1:47 PM
To: >
Subject: gpc-dev 10 May meeting?

I'm doing the usual agenda drill but I don't yet see enough stuff to merit a 
meeting.

If anybody has progress that they have not shared, please do so (it its own 
thread or ticket, not this one).

  *   gpc-dev 10 May shared meeting 
notes;
 scribe: MCW

--
Dan

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PROD_P02_DQA_FDPRO_DIAQ_NSD6_r001 SAS query

[Kowalski, George]

All, 

The SAS script references a   HARVEST table . In this table what are the 
NETWORKID , NETWORK_NAME, DATAMARTID and DATAMART_NAME we should be using ? 

Thanks

G

George Kowalski 
Biomedical Informatics Software Engineer
Clinical & Translational Science Institute
Medical College of Wisconsin
9200 West Wisconsin Avenue, Suite L722A
Milwaukee, Wisconsin USA 53226
 414.805.7318 (office) / gkowal...@mcw.edu



smime.p7s
Description: S/MIME cryptographic signature
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Re: data issues

[Kowalski, George]

Bradley,

W   When you say there are “ Duplicate records (indicated with equivalent 
sequence number”, what field are you basing this off of ? 
http://www.naaccr.org/Applications/ContentReader/default.aspx?c=9 shows  only 
two sequence numbers , both with not enough room to make each tumor unique .

[cid:B0AA3B86-D2F3-40F2-B462-3E055238E77C]

and

[cid:A6D5DCC0-5C33-46C4-8DD1-08D83F723388]

George Kowalski
 414.805.7318 (office) / gkowal...@mcw.edu

From: 
> 
on behalf of "McDowell, Bradley D" 
>
Date: Monday, February 1, 2016 at 11:00 AM
To: "gpc-dev@listserv.kumc.edu" 
>
Subject: FW: data issues

Dan asked me to forward this message to this group:

From: McDowell, Bradley D
Sent: Tuesday, January 26, 2016 11:00 AM
To: Dan Connolly (dconno...@kumc.edu)
Cc: Chrischilles, Elizabeth A; Gryzlak, Brian M
Subject: data issues

Hi Dan,

Betsy asked me to provide a list of the issues that have been uncovered so far 
with respect to the oncology registry data. The hope is that we can establish 
tickets for each problem. There are some problems that are easy to describe, 
and some that are not so easy. Some of the easy ones:


· Missing MCW patient 
(https://informatics.gpcnetwork.org/trac/Project/ticket/453)

· Duplicate records (indicated with equivalent sequence number for same 
Study ID), some with updated surgery, class of case variables

· Some duplicate records have dx dates that appear to have been copied 
from last contact date (dx date not the same across duplicates)

· UMN switched | and : for NAACCR variables (not “*.Descriptor” 
variables)

For the duplicated records, I have put together a spreadsheet that nicely 
illustrates the problem, and I’m happy to share that. We’ll have to transfer it 
via redcap or some other secure means since it contains patient level data.

Regarding the not so easy issues:

· One problem concerns inconsistencies in coded values. For example, 
gpc_language has four different values for “English”. In general, UIOWA is not 
using the same descriptor values as other sites, and that accounts for most of 
these. It is not the only offender, however. MCW uses a different convention 
for seer_site_breast (as does UIOWA) and Race descriptors are different for 
UIOWA and WISC. These inconsistencies have percolated through to the derived 
GPC variables. I am writing a mapping program to handle this with the registry 
data we have received so far. I’m certainly willing to share what I have if it 
would help you.

· Another big problem concerns missing values. I have attached a report 
that provides the percentage of missing values, organized by site and variable. 
This illustrates, for example, that UIOWA has no data for the Race 5 variable 
(i.e., 100% of the values equal “NA”; this does NOT reflect cases where a value 
is assigned for the NAACCR code for ‘missing’). It also illustrates some other 
things that we have discussed; for example, sites that reported data for 
central sequence number did not report data for hospital sequence number (and 
vice versa).

o   UIOWA and MCRF appear to have the biggest problems with missing data.

· We also need to figure out why so many patients in our database do 
not appear to have tumors diagnosed between 01JAN2013 and 01MAY2014.

(General observation: You’ll notice that each of the NAACCR concepts correspond 
to two variables (e.g., N0670_Surg_Prim_Site and N0670_Surg_Prim_Site_D). Vince 
and I settled on this arrangement for the datamart. Since then, though, I’ve 
come to believe that the redundancy makes the database difficult to use. 
Perhaps we could keep that in mind for future data cuts.)

I’m very happy to work on these problems with you. Would you like to schedule a 
phone call to plan out how to approach these issues?

Thanks,

Brad


Bradley D. McDowell, Ph.D.
Director, Population Research Core
Holden Comprehensive Cancer Center

5240 MERF | The University of Iowa | Iowa City, IA | 52242
Office: 319-384-1768

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gpc-qa-quarterly repo updated 1/201/6

[Kowalski, George]

All ,

REPO has been updated with the latest Oracle code from Phillip  : 
https://bitbucket.org/gpcnetwork/gpc-qa-quarterly/

G


George Kowalski
Biomedical Informatics Software Engineer
Clinical & Translational Science Institute
Medical College of Wisconsin
9200 West Wisconsin Avenue, Suite L722A
Milwaukee, Wisconsin USA 53226
 414.805.7318 (office) / gkowal...@mcw.edu
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Re: Oracle QA Queries

[Kowalski, George]

All,

Try as I might, no permissions  to push this code to the 
https://bitbucket.org/gpcnetwork/gpc-qa-quarterly repo for me.  We’ll have to 
wait for Dan.

G

George Kowalski
 414.805.7318 (office) / gkowal...@mcw.edu

From: 
> 
on behalf of Phillip Reeder 
>
Date: Tuesday, January 19, 2016 at 10:45 AM
To: "gpc-dev@listserv.kumc.edu" 
>
Subject: Oracle QA Queries

I believe this has all of the updates changed to merges and semicolons added 
where needed for it to run in Oracle.

Phillip



UT Southwestern


Medical Center



The future of medicine, today.

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Clarification on permissions within the PCORNet queries

[Kowalski, George]

All, 

Just an FYI on the Query tool I wanted clarification on. 

From:  Sturtevant, Jessica
Date:  Friday, February 13, 2015 at 8:53 AM
To:  Kowalski, George
Cc:  LAUREL  VERHAGEN, Jenny Ibarra (jenny.iba...@duke.edu)
Subject:  RE: MCW Ready with ver 5 client

Hi George,

 

This is a very good question.  The DSSNI TF technical team receives query 
responses and results for the IBQ via the PCORnet DRN Query Tool.  The 
permissions for the DSSNI TF technical team are set in the Query Tool.

 

If you have any further questions, please let me know.

 

Best,

 

Jessica

 

From: Kowalski, George [mailto:gkowal...@mcw.edu] 
Sent: Wednesday, February 11, 2015 3:26 PM
To: Sturtevant,Jessica
Cc: Verhagen, Laurel A
Subject: Re: MCW Ready with ver 5 client

 

Jessica, 

 

   When we submit our results who has access to them ? To 
members of the GPC , or you  . ? I ask as it appears to have been 
submitted  by you. 

 

G



smime.p7s
Description: S/MIME cryptographic signature
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Re: PopMedNet node at UNMC

[Kowalski, George]

Laurel,

I have the 5.0 DataMart  client connected to the:  https://api.pcornet.org 
Service URL and it seems to be working like the first time . Assuming we don’t 
have to hook it up to the “fake Postgres” data,  we’re ready to go here at MCW 
for the Basic Query.

Thanks

George

From: Justin Dale jd...@umn.edumailto:jd...@umn.edu
Date: Tuesday, February 10, 2015 at 7:24 PM
To: LAUREL VERHAGEN 
verhagen.lau...@mcrf.mfldclin.edumailto:verhagen.lau...@mcrf.mfldclin.edu
Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu 
gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: Re: PopMedNet node at UNMC

Minnesota DataMart client is working as expected thanks to help from Kyle.

Kyle said in his email:
If you have the DataMart Client installed and it appears to be functioning 
correctly, please let me know and I will notify the DSSNI team that you have 
everything in place to respond to the Initial Basic Query against the CDM.

Ashok and Laurel - did the DSSNI team send the request to you with the queries 
attached or did you download the queries and submit the query request to your 
datamart?



Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edumailto:jd...@umn.edu

On Mon, Feb 9, 2015 at 10:20 AM, Verhagen, Laurel A 
verhagen.lau...@mcrf.mfldclin.edumailto:verhagen.lau...@mcrf.mfldclin.edu 
wrote:
Ashok,

I have the same problem with the SQL server version that I’m trying to run. 
Sent an email to Jessica, but apparently the HPHCI offices are closed today due 
to weather.

Thanks,
Laurel

From: Mudgapalli, Ashok 
[mailto:ashok.mudgapa...@unmc.edumailto:ashok.mudgapa...@unmc.edu]
Sent: Monday, February 09, 2015 10:15 AM
To: Verhagen, Laurel A; Justin Dale

Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: RE: PopMedNet node at UNMC

If that is normal behavior, follow-up issue is …  I got the query file 
downloaded (zip file) and try to unzip, I am not able to unzip I tried many 
ways to unzip), the system says that the *.zip is invalid.  The file is oracle 
based query. Thanks.

Ashok

From: Verhagen, Laurel A [mailto:verhagen.lau...@mcrf.mfldclin.edu]
Sent: Monday, February 09, 2015 9:52 AM
To: Justin Dale; Mudgapalli, Ashok
Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: RE: PopMedNet node at UNMC

Justin is correct. Instructions are to download the queries, run locally, then 
upload. This is different than the first connectivity test.

Thanks,
Laurel

From:gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu
 [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Justin Dale
Sent: Monday, February 09, 2015 9:41 AM
To: Mudgapalli, Ashok
Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: Re: PopMedNet node at UNMC

We're seeing same screen when trying to edit the data model settings.   I'm 
wondering if this is the intended behavior since these are all file 
distribution queries and we're supposed to open the file and run against the 
CDM through whichever mechanism we choose and then attach the results to the 
request?  Not sure about all of this - suggest discussing in tomorrow's call.

[Inline image 1]

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747tel:612.624.9747
Fax: 612.624.7458tel:612.624.7458
jd...@umn.edumailto:jd...@umn.edu

On Mon, Feb 9, 2015 at 9:14 AM, Mudgapalli, Ashok 
ashok.mudgapa...@unmc.edumailto:ashok.mudgapa...@unmc.edu wrote:
We were able install the Popmednet 5.0 version of the data mart client and 
connect to the PCORnet network.  We are able to receive the “file distribution” 
query into our Data Mart client but unable to configure local Data Mart to 
execute the query for following reason. If you happen to know the solution or 
came across this issue please let me know. I sent an email to support team and 
waiting for the response.
My local data mart is on Oracle.
I did as follows:
DataMart Client -- Settings - Edit -- highlighted our DataMart 
(C4-University of Nebraska Medical … -- Edit -- DataMart Settings dialog has
[cid:image002.jpg@01D04452.0140DEE0]
Clicked on Edit and it showed no model processor.
[cid:image003.jpg@01D04452.0140DEE0]





Ashok Mudgapalli, MS, Ph.D.
Director of Research IT (Vice Chancellor for Research Office)
Assistant Professor
Genetics, Cell Biology, and Anatomy
College of Medicine
University of Nebraska Medical Center
Omaha, NE 68198-7878
402-559-9072tel:402-559-9072


The information in this e-mail may be privileged and confidential, intended 
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Re: agenda gpc-dev 8 Apr 11amCT

[Kowalski, George]

All,

Online Meeting notes for the 11:00am meeting can be found here :

http://bit.ly/1eopWKE


George Kowalski
Biomedical Informatics Software Engineer
Clinical  Translational Science Institute
Medical College of Wisconsin
9200 West Wisconsin Avenue, Suite L722A
Milwaukee, Wisconsin USA 53226
 414.805.7318 (office) / gkowal...@mcw.edumailto:gkowal...@mcw.edu







On Apr 7, 2014, at 1:41 PM, Dan Connolly 
dconno...@kumc.edumailto:dconno...@kumc.edu wrote:

We're unlikely to have time for all of these tomorrow, so if you want to make 
sure we get to something that's currently toward the end of the list, please 
let me know.

  1.  Convene, take roll, review records and plan next meeting
 *   ​Meeting ID and access code: 
686-845-717https://global.gotomeeting.com/meeting/join/686845717 call +1 
(267) 507-0008
 *   Scribe 
(#12https://informatics.gpcnetwork.org/trac/Project/ticket/12): MCW. @@ 
google doc
 *   roll: all 10 
DevTeamshttps://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams 
represented? comments on the agenda?
*   KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, UTSW
*   a number of new/closed 
ticketshttps://informatics.gpcnetwork.org/trac/Project/timeline are on 
today's agenda
 *   ​1 Apr meeting 
noteshttp://listserv.kumc.edu/pipermail/gpc-dev/2014q2/54.html OK?
 *   Proposed: to meet again Tue, 15 Apr 2014 11amCT; UIOWA to scribe.
  2.  #87https://informatics.gpcnetwork.org/trac/Project/ticket/87 Deploy, 
document R Data Builder demo service
 *   quick update
  3.  #55https://informatics.gpcnetwork.org/trac/Project/ticket/55 (source of 
idx_table not portable) closed wontfix
 *   FYI; note partial info
  4.  de-identification plan 
(#73https://informatics.gpcnetwork.org/trac/Project/ticket/73)
 *   update from Tom M. from PCORI privacy TF 1 Apr meeting
 *   confirm 10 Apr 
milestone:deid-planhttps://informatics.gpcnetwork.org/trac/Project/milestone/deid-plan
 due date or reschedule
  5.  #103https://informatics.gpcnetwork.org/trac/Project/ticket/103 (subject 
of observation (e.g. maternal findings relevant to child)) created
  6.  #97https://informatics.gpcnetwork.org/trac/Project/ticket/97 
(Characterize enrollment for PCORI Milestone 1.1) created
  7.  #98https://informatics.gpcnetwork.org/trac/Project/ticket/98 (babel 
seems at times slow to open folders) closed fixed
 *   FYI re demos last week
  8.  i2b2 demo by UNMC
  9.  #94https://informatics.gpcnetwork.org/trac/Project/ticket/94 
(Deprecated fields used in diagnosis extracts) closed
  10. HERON monthly refresh strategy and the approach of switching users 
between two instances. (Feb 27 request from Marshfield)
  11. i2b2 demo by UMN (or CMH or MCRF)
  12. #102https://informatics.gpcnetwork.org/trac/Project/ticket/102 (How do 
we represent patient reported outcomes?) created

--
Dan

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