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

[Pedersen, Jay G]

Hi,


A "contrib" repo in SCILHS works for me.  It gives me a place to put this ... 
and a place for you to take a look at it, etc.

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)

From: Klann, Jeffrey G. 
Sent: Monday, April 24, 2017 9:58:00 PM
To: Pedersen, Jay G; Dan Connolly
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Michael Prittie; 
Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Might make more sense for you guys to have your own GitHub for the time being, 
and we could link to it. Or if you prefer, I’d be happy to set up a “contrib” 
repo in SCILHS that you could commit to.

Thanks,
Jeff Klann

From: "Pedersen, Jay G" 
Date: Monday, April 24, 2017 at 10:28 PM
To: Dan Connolly 
Cc: Hubert Hickman , Russ Waitman 
, "gpc-dev@listserv.kumc.edu" , 
Jeffrey KLANN , Michael Prittie 
, "Campbell, James R" 
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient


Hi,



I wasn't sure where to put the code in github.  I believe we are glad to share 
the code, which is written in

python and uses web services from the NLM and an input file with history 
information of RxNorm codes received from the NLM.



Where would be the appropriate spot to put that?  I thought it was supposed to 
go to the SCILHS github.


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)

From: Dan Connolly 
Sent: Monday, April 24, 2017 8:56:13 PM
To: Pedersen, Jay G
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Klann, Jeffrey G.; 
Michael Prittie; Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G"  wrote:

Hi,



The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.



I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.



The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.



Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):



https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]



https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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)


From: Klann, Jeffrey G. 
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, I have not seen it either. Please point us to it, thanks.

On 4/24/17, 11:59 AM, "GPC Informatics"  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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informati

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

[Klann, Jeffrey G.]

Might make more sense for you guys to have your own GitHub for the time being, 
and we could link to it. Or if you prefer, I’d be happy to set up a “contrib” 
repo in SCILHS that you could commit to.

Thanks,
Jeff Klann

From: "Pedersen, Jay G" 
Date: Monday, April 24, 2017 at 10:28 PM
To: Dan Connolly 
Cc: Hubert Hickman , Russ Waitman 
, "gpc-dev@listserv.kumc.edu" , 
Jeffrey KLANN , Michael Prittie 
, "Campbell, James R" 
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient


Hi,



I wasn't sure where to put the code in github.  I believe we are glad to share 
the code, which is written in

python and uses web services from the NLM and an input file with history 
information of RxNorm codes received from the NLM.



Where would be the appropriate spot to put that?  I thought it was supposed to 
go to the SCILHS github.


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)

From: Dan Connolly 
Sent: Monday, April 24, 2017 8:56:13 PM
To: Pedersen, Jay G
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Klann, Jeffrey G.; 
Michael Prittie; Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G"  wrote:

Hi,



The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.



I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.



The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.



Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):



https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]



https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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)


From: Klann, Jeffrey G. 
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, I have not seen it either. Please point us to it, thanks.

On 4/24/17, 11:59 AM, "GPC Informatics"  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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics




The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

The information in this e-mail may be privileged and confidential, intended 
only for the use of the addressee(s) above. Any unauthorized use or disclosure 
of this information is prohibited. If you have re

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

[Pedersen, Jay G]

Hi,


I wasn't sure where to put the code in github.  I believe we are glad to share 
the code, which is written in

python and uses web services from the NLM and an input file with history 
information of RxNorm codes received from the NLM.


Where would be the appropriate spot to put that?  I thought it was supposed to 
go to the SCILHS github.

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)

From: Dan Connolly 
Sent: Monday, April 24, 2017 8:56:13 PM
To: Pedersen, Jay G
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Klann, Jeffrey G.; 
Michael Prittie; Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G"  wrote:

Hi,


The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.


I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.


The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.


Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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)


From: Klann, Jeffrey G. 
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, I have not seen it either. Please point us to it, thanks.

On 4/24/17, 11:59 AM, "GPC Informatics"  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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics




The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

The information in this e-mail may be privileged and confidential, intended 
only for the use of the addressee(s) above. Any unauthorized use or disclosure 
of this information is prohibited. If you have received this e-mail by mistake, 
please delete it and immediately contact the sender.


The information in this e-mail may be privileged and confidential, intended 
only for the use of the addressee(s) above. Any unauthorized use or disclosure 
of this information is prohibited. If you have received this e-mail by mistake, 
please delete it and immediately contact the sender.
___
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http://listserv.kumc.edu/mailman/listinfo/gpc-de

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

[Dan Connolly]

Yes, it's on babel. But Jim wrote that you were sharing it via git as well. Not 
so?

On Apr 24, 2017 7:44 PM, "Pedersen, Jay G"  wrote:

Hi,


The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.


I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.


The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.


Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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)


From: Klann, Jeffrey G. 
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, I have not seen it either. Please point us to it, thanks.

On 4/24/17, 11:59 AM, "GPC Informatics"  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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics




The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

The information in this e-mail may be privileged and confidential, intended 
only for the use of the addressee(s) above. Any unauthorized use or disclosure 
of this information is prohibited. If you have received this e-mail by mistake, 
please delete it and immediately contact the sender.

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

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

[Pedersen, Jay G]

Hi,


The Medication ontology exists in BABEL, at folder UNMC: SCILHS, in the 
Medications subfolder.


I tried it moments ago, and it still opened VERY slow.  So ... I include links 
to a couple

of pictures taken from BABEL that shows the metadata -- from the VA class level 
through

the RxNorm code level for ingredients and orderable drugs down to the NDC code 
level

for packaged drugs.


The 'VA class' hierarchy is the first subfolder of Medications, and we also have

a second which has the ingredients in alphabetical order.  We have a folder for

letters A through Z.  Taking any of these folders lists the ingredients which 
start

with that letter, and underneath of ingredients lie the orderable drugs and the

drug packages.


Links to BABEL pictures of SCILHS Medications Ontology (NOTE: there are quite a 
rows for modifiers (blue dot rows), that repeat at each level,

and can be hidden by modifying their C_VISUALATTRIBUTES if they don't apply at 
any particular site):


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p1.png]


https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png

[https://dl.dropboxusercontent.com/u/5167630/UNMC_SCILHS_MEDS_p2.png]

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)


From: Klann, Jeffrey G. 
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R; 
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

Yes, I have not seen it either. Please point us to it, thanks.

On 4/24/17, 11:59 AM, "GPC Informatics"  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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics




The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

The information in this e-mail may be privileged and confidential, intended 
only for the use of the addressee(s) above. Any unauthorized use or disclosure 
of this information is prohibited. If you have received this e-mail by mistake, 
please delete it and immediately contact the sender.
___
Gpc-dev mailing list
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RE: U of Missouri HC's r004 approved

[Mosa, Abu S.]

Thanks Russ.

Regards,
Dr. Abu Saleh Mohammad Mosa, MS, PhD
Director, Research Informatics
University of Missouri School of Medicine
Assistant Research Professor of Health Informatics
Health Management and Informatics
One Hospital Drive, NW505, DC018.00
Columbia, MO 65212
Phone: 573-882-8349
Email: mo...@health.missouri.edu
Web: medicine.missouri.edu | hmi.missouri.edu



From: Parker, Jerry C.
Sent: Monday, April 24, 2017 1:58 PM
To: Russ Waitman ; Mosa, Abu S. ; 
Laurel Verhagen ; greenlee.robert 

Cc: GPC-DEV@LISTSERV.KUMC.EDU
Subject: RE: U of Missouri HC's r004 approved

Just super!  Jerry

From: Russ Waitman [mailto:rwait...@kumc.edu]
Sent: Monday, April 24, 2017 1:50 PM
To: Mosa, Abu S. mailto:mo...@health.missouri.edu>>; 
Laurel Verhagen 
mailto:verhagen.lau...@mcrf.mfldclin.edu>>; 
greenlee.robert 
mailto:greenlee.rob...@mcrf.mfldclin.edu>>
Cc: GPC-DEV@LISTSERV.KUMC.EDU; Parker, Jerry 
C. mailto:parke...@health.missouri.edu>>
Subject: RE: U of Missouri HC's r004 approved

Great news Mosa!

Russ


From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Monday, April 24, 2017 1:18 PM
To: Mosa, Abu S.; Laurel Verhagen; greenlee.robert; Russ Waitman
Cc: James Topping; Laura Qualls; Darcy Louzao, Ph.D.
Subject: U of Missouri HC's r004 approved

Good afternoon.

I’m happy to report that C4UMO's data characterization query response for 
refresh 4 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: Indiana Regenstrief's r005 approved

[Grannis, Shaun J]

Excellent news! Thanks to Bill, Tony, and everyone involved in making this 
happen.

Thank you,

Shaun

From: Russ Waitman 
Date: Monday, April 24, 2017 at 3:59 PM
To: "French, Tony" , "Hood, Daniel Robert" 
, Laurel Verhagen , 
"greenlee.robert" 
Cc: "Barnett, William Kinne" , "Grannis, Shaun J" 
, "GPC-DEV@LISTSERV.KUMC.EDU" 

Subject: RE: Indiana Regenstrief's r005 approved

Congrats Tony and Dan,


Russ Waitman, PhD
Director of Medical Informatics
Associate Vice Chancellor for Enterprise Analytics
Professor, Department of Internal Medicine
University of Kansas Medical Center, Kansas City, Kansas
913-945-7087 (office)
rwait...@kumc.edu
http://www.kumc.edu/ea-mi/
http://informatics.kumc.edu
http://informatics.gpcnetwork.org – a 
PCORnet collaborative



From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Monday, April 24, 2017 2:51 PM
To: adfre...@regenstrief.org; danh...@regenstrief.org; Laurel Verhagen; 
greenlee.robert; Russ Waitman
Cc: James Topping; Laura Qualls; Darcy Louzao, Ph.D.
Subject: Indiana Regenstrief's r005 approved

Good afternoon.

I’m happy to report that C4REG's data characterization query response for 
refresh 5 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: Indiana Regenstrief's r005 approved

[Russ Waitman]

Congrats Tony and Dan,


Russ Waitman, PhD
Director of Medical Informatics
Associate Vice Chancellor for Enterprise Analytics
Professor, Department of Internal Medicine
University of Kansas Medical Center, Kansas City, Kansas
913-945-7087 (office)
rwait...@kumc.edu
http://www.kumc.edu/ea-mi/
http://informatics.kumc.edu
http://informatics.gpcnetwork.org – a 
PCORnet collaborative



From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Monday, April 24, 2017 2:51 PM
To: adfre...@regenstrief.org; danh...@regenstrief.org; Laurel Verhagen; 
greenlee.robert; Russ Waitman
Cc: James Topping; Laura Qualls; Darcy Louzao, Ph.D.
Subject: Indiana Regenstrief's r005 approved

Good afternoon.

I’m happy to report that C4REG's data characterization query response for 
refresh 5 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: U of Missouri HC's r004 approved

[Parker, Jerry C.]

Just super!  Jerry

From: Russ Waitman [mailto:rwait...@kumc.edu]
Sent: Monday, April 24, 2017 1:50 PM
To: Mosa, Abu S. ; Laurel Verhagen 
; greenlee.robert 

Cc: GPC-DEV@LISTSERV.KUMC.EDU; Parker, Jerry C. 
Subject: RE: U of Missouri HC's r004 approved

Great news Mosa!

Russ


From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Monday, April 24, 2017 1:18 PM
To: Mosa, Abu S.; Laurel Verhagen; greenlee.robert; Russ Waitman
Cc: James Topping; Laura Qualls; Darcy Louzao, Ph.D.
Subject: U of Missouri HC's r004 approved

Good afternoon.

I’m happy to report that C4UMO's data characterization query response for 
refresh 4 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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AdapterMappings: why 1-to-many?

[Dan Connolly]

Why do some entries in `AdapterMappings.xml` have more than one value? For 
example:



\\SHRINE\i2b2\Demographics\Age\


\\HIMC_DEMOGRAPHICS\i2b2\Demographics\Age\0-9 years old\

\\HIMC_DEMOGRAPHICS\i2b2\Demographics\Age\10-17 years 
old\

\\HIMC_DEMOGRAPHICS\i2b2\Demographics\Age\18-34 years 
old\

Doesn't it suffice to map the Age folder to the Age folder?

The only documentation I see is 
https://open.med.harvard.edu/wiki/display/SHRINE/Implementation ; is there more 
somewhere?

Are these mappings loaded into a database table? Or are they read from a file 
at run-time?

--
Dan

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RE: U of Missouri HC's r004 approved

[Russ Waitman]

Great news Mosa!

Russ


From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Monday, April 24, 2017 1:18 PM
To: Mosa, Abu S.; Laurel Verhagen; greenlee.robert; Russ Waitman
Cc: James Topping; Laura Qualls; Darcy Louzao, Ph.D.
Subject: U of Missouri HC's r004 approved

Good afternoon.

I’m happy to report that C4UMO's data characterization query response for 
refresh 4 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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gpc-dev 25 Apr agenda and meeting notes

[Dan Connolly]

What else for tomorrow? It's pretty quiet out there... :)


  *   25 Apr gpc-dev shared 
notes;
 scribe: UMN




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

 *   11:00am Central Time.
​Meeting ID and access code: 
817-393-381; call +1 
(571) 317-3131

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

*   today's scribe: UMN

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

*   #594 (babel ontology update for MU) created by 
tmcneeley

*   #46 (establish gpc-dev text chat, regular discussion) 
reopened: 
The #gpc-dev IRC channel has fallen below critical mass;

*   #593 (Please load the MCW terms file into Babel) 
created

 *   Next Meeting: 2 May; scribe: UTSW? WISC?

*   Note LRU scribe schedule in 
#12

  1.  
Milestone:cdm-c2r2
 due 24 Apr

 *   #580 Data 
Characterization - Cycle 2, Refresh 2 
Tracking

*   Sites approved (yay!): UNMC, WISC, MCW, CMH

*   Submitted: KUMC, ??

*   Not submitted: ??

  2.  Milestone:adaptable-monitor
#478
 ADAPTABLE 
monitoring: Laura 
Qualls just put ADPT_AHR_WP002_NSD_B02.zip on imeet central: DRN OC 
ADAPTABLE
 folder

  3.  
Milestone:next-d
 due 9 May

  4.  
Milestone:snow-shrine-1
 due 15 May, snow-shrine-2
Due 
date revised.


--
Dan

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

[Klann, Jeffrey G.]

Yes, I have not seen it either. Please point us to it, thanks.

On 4/24/17, 11:59 AM, "GPC Informatics"  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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics




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Re: [gpc-informatics] #583: SNOW SCILHS Lab Metadata Expansion

[GPC Informatics]

#583: SNOW SCILHS Lab Metadata Expansion
---+---
 Reporter:  campbell   |   Owner:  campbell
 Type:  enhancement|  Status:  assigned
 Priority:  major  |   Milestone:  snow-
Component:  data-stds  |  shrine-2
 Keywords:  LOINC Lab_PRO_CM SCILHS all-sites  |  Resolution:
 Blocking: |  Blocked By:
---+---

Comment (by dconnolly):

 in Apr 18 gpc-dev (#12):
 JRC: MCW and UTHSCSA replied with their codes and we’re building the
 metadata now. Hope for a review in a week or two.

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

[GPC Informatics]

#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:  all-sites|  Blocked By:  568, 592
 Blocking:   |
-+

Comment (by dconnolly):

 Campbell writes Wednesday, April 12, 2017 6:27 PM
 > Jay is pushing a copy along with documentation up to your GITHUB site
 for you and the SCILHS community to comment.

 Jay, point us to the results of that push? URL? commit hash?

--
Ticket URL: 

gpc-informatics 
Greater Plains Network - Informatics
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FW: Children's Mercy's r004 approved

[Fothergill, Rita, R]

CMH is approved.

From: PCORnet DRN OC [mailto:dr...@pcornet.org]
Sent: Monday, April 24, 2017 10:44 AM
To: Fothergill, Rita, R ; Laurel Verhagen 
; greenlee.robert 
; Russ Waitman 
Cc: James Topping ; Laura Qualls 
; Darcy Louzao, Ph.D. 
Subject: Children's Mercy's r004 approved

*** This message was sent to you from an External Source. Please do not open 
untrusted links or attachments. ***


Good morning.

I’m happy to report that C4CMH's data characterization query response for 
refresh 4 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



Electronic mail from Children's Mercy Kansas City. This communication is 
intended only for the use of the addressee. It may contain information that is 
privileged or confidential under applicable law. If you are not the intended 
recipient or the agent of the recipient, you are hereby notified that any 
dissemination, copy or disclosure of this communication is strictly prohibited. 
If you have received this communication in error, please immediately forward 
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Re: Med Coll Wisconsin's r003 approved

[Russ Waitman]

Awesome!

Russ Waitman 


> On Apr 24, 2017, at 9:00 AM, Kowalski, George  wrote:
> 
> We’ve been approved.
> 
> From: "Kowalski, George" 
> Date: Monday, April 24, 2017 at 8:44 AM
> To: CRDW 
> Subject: FW: Med Coll Wisconsin's r003 approved
> 
> 
> 
> From: PCORnet DRN OC 
> Date: Monday, April 24, 2017 at 8:43 AM
> To: "Osinski, Kristen" , "Kowalski, George" 
> , LAUREL VERHAGEN , 
> "greenlee.robert" , Russ Waitman 
> 
> Cc: Laura Qualls , "Darcy Louzao, Ph.D." 
> , James Topping 
> 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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FW: Med Coll Wisconsin's r003 approved

[Kowalski, George]

We’ve been approved.

From: "Kowalski, George" 
Date: Monday, April 24, 2017 at 8:44 AM
To: CRDW 
Subject: FW: Med Coll Wisconsin's r003 approved



From: PCORnet DRN OC 
Date: Monday, April 24, 2017 at 8:43 AM
To: "Osinski, Kristen" , "Kowalski, George" 
, LAUREL VERHAGEN , 
"greenlee.robert" , Russ Waitman 

Cc: Laura Qualls , "Darcy Louzao, Ph.D." 
, James Topping 
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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