Re: SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request [was: gpc-dev July 14 agenda]

2020-07-13 Thread Campbell, James R 
If a GPC site is using Epic, and if the site has deployed IMO as their 
terminology intermediary then Nebraska can provide the SQL code that would pull 
the SNOMED CT diagnoses from their CONDITION and (possibly) their DIAGNOSIS 
tables
Jim Campbell

From: Gpc-dev  on behalf of Campbell, James 
R 
Sent: Monday, July 13, 2020 1:20 PM
To: Russ Waitman ; Dan Connolly ; Roush, 
Steffani 
Cc: gpc-dev@listserv.kumc.edu 
Subject: Re: SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request 
[was: gpc-dev July 14 agenda]

Non-UNMC email
Nebraska has records on 18 patients with problem list/CONDITION entry of 
5619004|Bardet-Biedl syndrome (disorder)|
Jim Campbell

From: Gpc-dev  on behalf of Russ Waitman 

Sent: Monday, July 13, 2020 12:45 PM
To: Dan Connolly ; Roush, Steffani 

Cc: gpc-dev@listserv.kumc.edu 
Subject: Re: SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request 
[was: gpc-dev July 14 agenda]

Non-UNMC email

FYI,

I may miss the call but we mainly have them in diagnoses facts in i2b2 under 
parent ICD10 codes listed with DX_IDs from IMO. We also have a goal to work 
with the network to come up with best practices for placing them in either DX 
or Condition tables appropriately for another proposal and was discussing Mei 
today.



So bottom line, we could likely run the query here against i2b2,



Russ



From: Gpc-dev  on behalf of Dan Connolly 

Date: Monday, July 13, 2020 at 1:20 PM
To: "roush.steff...@marshfieldresearch.org" 

Cc: "GPC-DEV@LISTSERV.KUMC.EDU" 
Subject: SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request [was: 
gpc-dev July 14 agenda]









From: Roush, Steffani 
Sent: Monday, July 13, 2020 12:42 PM
To: Dan Connolly 
Subject: RE: gpc-dev July 14 agenda and meeting notes



Hi Dan,



Can you add something to the agenda for me? I would add it myself, but MCHS IS 
recently revoked my access to google docs, and I’m still trying to get an 
internet override request approved…



Topic:



Bardet-Biedel Syndrome (BBS) Request

•Dr. VanWormer and Dr. Haws at Marshfield are looking to put in a 
proposal for a study relating to BBS

•Numbers are needed from GPC to see if we have sufficient population

o   ICD 9/10 codes are too vague and not specific to this condition

o   There is a SNOMED code (5619004) specific to BBS that may potentially be 
used

•  Do sites in GPC fill their Condition and Diagnosis CDM tables with SNOMED 
codes?

•  If not, how difficult would it be for sites to identify the number of 
patients with this condition using document searches/NLP?

•Ideas needed for getting these counts from all of PCORnet

o   If sites have this SNOMED code in their CDM then this will be much easier 
to accomplish than if sites need to use NLP



Thanks,





[image006]Steffani Roush

Research Programmer Analyst Senior | Office of Research Computing and Analytics

Marshfield Clinic Research Institute

Office: 715-221-6442 | Ext: 1-6442



From: Gpc-dev  On Behalf Of Dan Connolly
Sent: Monday, July 13, 2020 10:15 AM
To: gpc-dev@listserv.kumc.edu
Subject: [EXTERNAL] gpc-dev July 14 agenda and meeting notes



CAUTION: This email originated from outside of the Marshfield Clinic Health 
System. Do not click links or open attachments unless you recognize the sender 
and know the content is safe.



What else for tomorrow?



UNMC is scheduled to scribe

https://docs.google.com/document/d/1Bs0kkY7wI9SPZnmQBHEg9lfNDzuS-T2M_MJoT-aAajk/edit



agenda snapshot:



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

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

b. Roll; Reminder - put site after your name in 
GoToMeeting
 preferences
GPC 
DevTeams
 represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC (scribe), UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

c. Comments on the agenda? (ref 
SoftwareDev#tracking)
 On

Re: SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request [was: gpc-dev July 14 agenda]

2020-07-13 Thread Campbell, James R 
Nebraska has records on 18 patients with problem list/CONDITION entry of 
5619004|Bardet-Biedl syndrome (disorder)|
Jim Campbell

From: Gpc-dev  on behalf of Russ Waitman 

Sent: Monday, July 13, 2020 12:45 PM
To: Dan Connolly ; Roush, Steffani 

Cc: gpc-dev@listserv.kumc.edu 
Subject: Re: SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request 
[was: gpc-dev July 14 agenda]

Non-UNMC email

FYI,

I may miss the call but we mainly have them in diagnoses facts in i2b2 under 
parent ICD10 codes listed with DX_IDs from IMO. We also have a goal to work 
with the network to come up with best practices for placing them in either DX 
or Condition tables appropriately for another proposal and was discussing Mei 
today.



So bottom line, we could likely run the query here against i2b2,



Russ



From: Gpc-dev  on behalf of Dan Connolly 

Date: Monday, July 13, 2020 at 1:20 PM
To: "roush.steff...@marshfieldresearch.org" 

Cc: "GPC-DEV@LISTSERV.KUMC.EDU" 
Subject: SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request [was: 
gpc-dev July 14 agenda]









From: Roush, Steffani 
Sent: Monday, July 13, 2020 12:42 PM
To: Dan Connolly 
Subject: RE: gpc-dev July 14 agenda and meeting notes



Hi Dan,



Can you add something to the agenda for me? I would add it myself, but MCHS IS 
recently revoked my access to google docs, and I’m still trying to get an 
internet override request approved…



Topic:



Bardet-Biedel Syndrome (BBS) Request

•Dr. VanWormer and Dr. Haws at Marshfield are looking to put in a 
proposal for a study relating to BBS

•Numbers are needed from GPC to see if we have sufficient population

o   ICD 9/10 codes are too vague and not specific to this condition

o   There is a SNOMED code (5619004) specific to BBS that may potentially be 
used

•  Do sites in GPC fill their Condition and Diagnosis CDM tables with SNOMED 
codes?

•  If not, how difficult would it be for sites to identify the number of 
patients with this condition using document searches/NLP?

•Ideas needed for getting these counts from all of PCORnet

o   If sites have this SNOMED code in their CDM then this will be much easier 
to accomplish than if sites need to use NLP



Thanks,





[image006]Steffani Roush

Research Programmer Analyst Senior | Office of Research Computing and Analytics

Marshfield Clinic Research Institute

Office: 715-221-6442 | Ext: 1-6442



From: Gpc-dev  On Behalf Of Dan Connolly
Sent: Monday, July 13, 2020 10:15 AM
To: gpc-dev@listserv.kumc.edu
Subject: [EXTERNAL] gpc-dev July 14 agenda and meeting notes



CAUTION: This email originated from outside of the Marshfield Clinic Health 
System. Do not click links or open attachments unless you recognize the sender 
and know the content is safe.



What else for tomorrow?



UNMC is scheduled to scribe

https://docs.google.com/document/d/1Bs0kkY7wI9SPZnmQBHEg9lfNDzuS-T2M_MJoT-aAajk/edit



agenda snapshot:



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

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

b. Roll; Reminder - put site after your name in 
GoToMeeting
 preferences
GPC 
DevTeams
 represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC (scribe), UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

c. Comments on the agenda? (ref 
SoftwareDev#tracking)
 On last week’s 
notes?
 
(#12)
Recent tickets

Re: SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request [was: gpc-dev July 14 agenda]

2020-07-13 Thread Russ Waitman 
FYI,
I may miss the call but we mainly have them in diagnoses facts in i2b2 under 
parent ICD10 codes listed with DX_IDs from IMO. We also have a goal to work 
with the network to come up with best practices for placing them in either DX 
or Condition tables appropriately for another proposal and was discussing Mei 
today.

So bottom line, we could likely run the query here against i2b2,

Russ

From: Gpc-dev  on behalf of Dan Connolly 

Date: Monday, July 13, 2020 at 1:20 PM
To: "roush.steff...@marshfieldresearch.org" 

Cc: "GPC-DEV@LISTSERV.KUMC.EDU" 
Subject: SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request [was: 
gpc-dev July 14 agenda]




From: Roush, Steffani 
Sent: Monday, July 13, 2020 12:42 PM
To: Dan Connolly 
Subject: RE: gpc-dev July 14 agenda and meeting notes


Hi Dan,



Can you add something to the agenda for me? I would add it myself, but MCHS IS 
recently revoked my access to google docs, and I’m still trying to get an 
internet override request approved…



Topic:



Bardet-Biedel Syndrome (BBS) Request

•Dr. VanWormer and Dr. Haws at Marshfield are looking to put in a 
proposal for a study relating to BBS

•Numbers are needed from GPC to see if we have sufficient population

o   ICD 9/10 codes are too vague and not specific to this condition

o   There is a SNOMED code (5619004) specific to BBS that may potentially be 
used

•  Do sites in GPC fill their Condition and Diagnosis CDM tables with SNOMED 
codes?

•  If not, how difficult would it be for sites to identify the number of 
patients with this condition using document searches/NLP?

•Ideas needed for getting these counts from all of PCORnet

o   If sites have this SNOMED code in their CDM then this will be much easier 
to accomplish than if sites need to use NLP



Thanks,





[image006]Steffani Roush

Research Programmer Analyst Senior | Office of Research Computing and Analytics

Marshfield Clinic Research Institute

Office: 715-221-6442 | Ext: 1-6442



From: Gpc-dev  On Behalf Of Dan Connolly
Sent: Monday, July 13, 2020 10:15 AM
To: gpc-dev@listserv.kumc.edu
Subject: [EXTERNAL] gpc-dev July 14 agenda and meeting notes



CAUTION: This email originated from outside of the Marshfield Clinic Health 
System. Do not click links or open attachments unless you recognize the sender 
and know the content is safe.




What else for tomorrow?



UNMC is scheduled to scribe

https://docs.google.com/document/d/1Bs0kkY7wI9SPZnmQBHEg9lfNDzuS-T2M_MJoT-aAajk/edit



agenda snapshot:



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

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

b. Roll; Reminder - put site after your name in 
GoToMeeting
 preferences
GPC 
DevTeams
 represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC (scribe), UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

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

   i.  None this week

d. Next meeting(s): Jul 21; scribe: UTHSCSA? UTSW?

.  Note scribe

SNOMED in Condition? for Bardet-Biedel Syndrome (BBS) Request [was: gpc-dev July 14 agenda]

2020-07-13 Thread Dan Connolly 



From: Roush, Steffani 
Sent: Monday, July 13, 2020 12:42 PM
To: Dan Connolly 
Subject: RE: gpc-dev July 14 agenda and meeting notes


Hi Dan,



Can you add something to the agenda for me? I would add it myself, but MCHS IS 
recently revoked my access to google docs, and I’m still trying to get an 
internet override request approved…



Topic:



Bardet-Biedel Syndrome (BBS) Request

·Dr. VanWormer and Dr. Haws at Marshfield are looking to put in a 
proposal for a study relating to BBS

·Numbers are needed from GPC to see if we have sufficient population

o   ICD 9/10 codes are too vague and not specific to this condition

o   There is a SNOMED code (5619004) specific to BBS that may potentially be 
used

§  Do sites in GPC fill their Condition and Diagnosis CDM tables with SNOMED 
codes?

§  If not, how difficult would it be for sites to identify the number of 
patients with this condition using document searches/NLP?

·Ideas needed for getting these counts from all of PCORnet

o   If sites have this SNOMED code in their CDM then this will be much easier 
to accomplish than if sites need to use NLP



Thanks,





[image006]Steffani Roush

Research Programmer Analyst Senior | Office of Research Computing and Analytics

Marshfield Clinic Research Institute

Office: 715-221-6442 | Ext: 1-6442



From: Gpc-dev  On Behalf Of Dan Connolly
Sent: Monday, July 13, 2020 10:15 AM
To: gpc-dev@listserv.kumc.edu
Subject: [EXTERNAL] gpc-dev July 14 agenda and meeting notes



CAUTION: This email originated from outside of the Marshfield Clinic Health 
System. Do not click links or open attachments unless you recognize the sender 
and know the content is safe.




What else for tomorrow?



UNMC is scheduled to scribe

https://docs.google.com/document/d/1Bs0kkY7wI9SPZnmQBHEg9lfNDzuS-T2M_MJoT-aAajk/edit



agenda snapshot:



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

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

b. Roll; Reminder - put site after your name in 
GoToMeeting
 preferences
GPC 
DevTeams
 represented? KUMC (chair), UIOWA, MCW, MCRI, UNMC (scribe), UTHSCSA, UTSW, MU, 
IndianaU, Utah, Allina, Intermountain, UTH

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

   i.  None this week

d. Next meeting(s): Jul 21; scribe: UTHSCSA? UTSW?

.  Note scribe 
rotation
 appendix

   i.  
#759
 covid19 PCORNet 
datamarts
 pause additional ETL development until PCORI completes