Re: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 2, 3

2017-07-17 Thread GPC Informatics
#596: targeted cancer therapy study - Query 1, 2, 3
--+
 Reporter:  dconnolly |   Owner:  schandaka
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+

Comment (by schandaka):

 KUMC's Query 2 and Query 3 data has been loaded into REDCap. We found none
 of the labs.

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Re: [gpc-informatics] #544: how to convert ACS raw variables to CAP variables (e.g. type of health insurance)?

2017-07-17 Thread Phillip Reeder
That is my understanding as well.  But if you have IRB approval for a
limited dataset, I think the tract could be part of a limited dataset
since it would not be considered a primary identifier of the patient.

Phillip


On 7/17/17, 1:54 PM, "Mei Liu"  wrote:

>Based on my limited understanding, ACS variables linked to a census tract
>contain aggregate/average information. But the census tract ID itself
>when linked to a patient record is PHI because it identifies a geographic
>location with <20,000 people. Am I interpreting this correctly?
>
>Mei
>
>-Original Message-
>From: Bernard Black [mailto:bbl...@kellogg.northwestern.edu]
>Sent: Monday, July 17, 2017 1:09 PM
>To: gpc-dev@listserv.kumc.edu; Dan Connolly; Mei Liu;
>furmanc...@icnanotox.org; kosin...@mcw.edu
>Cc: btay...@mcw.edu; vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook;
>Charon Gladfelter; Brennan Connolly; nicholas-c-sm...@uiowa.edu;
>phillip.ree...@utsouthwestern.edu; mo...@health.missouri.edu;
>danh...@regenstrief.org; Hillary Sandoval; George Kowalski
>Subject: RE: [gpc-informatics] #544: how to convert ACS raw variables to
>CAP variables (e.g. type of health insurance)?
>
>Census tract information *is* averaged, and is not PHI.
>That is why Census is willing to release it.
>
>Bernie
>*
>Bernard S. Black
>bbl...@northwestern.edu
>Nicholas D. Chabraja Professor, Northwestern University
> Pritzker School of Law
> Institute for Policy Research
> Kellogg School of Management, Finance Dep¹t Law School:  375 East
>Chicago Ave., Chicago IL 60611
>Kellogg:  2211 Campus Drive, Evanston IL 60208
>tel:  law:  312-503-2784; Kellogg:  847-491-5049; cell: 847-807-9599
>papers on SSRN at:  http://ssrn.com/author=16042
>
>
>-Original Message-
>From: GPC Informatics [mailto:d...@madmode.com]
>Sent: Monday, July 17, 2017 12:11 PM
>To: Dan Connelly ; mei...@kumc.edu;
>furmanc...@icnanotox.org; kosin...@mcw.edu
>Cc: btay...@mcw.edu; Bernard Black ;
>vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook
>; Charon Gladfelter
>; bconno...@kumc.edu;
>nicholas-c-sm...@uiowa.edu; phillip.ree...@utsouthwestern.edu;
>mo...@health.missouri.edu; danh...@regenstrief.org; hsando...@kumc.edu;
>George Kowalski 
>Subject: Re: [gpc-informatics] #544: how to convert ACS raw variables to
>CAP variables (e.g. type of health insurance)?
>
>#544: how to convert ACS raw variables to CAP variables (e.g. type of
>health insurance)?
>--+---
> Reporter:  dconnolly |   Owner:  meiliu
> Type:  design-issue  |  Status:  assigned
> Priority:  major |   Milestone:  next-d
>Component:  data-stds |  Resolution:
> Keywords:|  Blocked By:
> Blocking:  598   |
>--+---
>
>Comment (by meiliu):
>
> Our most recent IRB protocol is in the attachment.
> - As noted in the protocol, "...variables such as income, educational
>attainment, likelihood of employment, poverty status, owner-occupied
>house  value, and health insurance coverage derived from geocoded address
>data  will be used only as average values, not tied to any specific
>individual  but rather to study populations."
> - I did not find any language on sharing census tract information.
> I've discussed this with Tamara McMahon and agree that since census
>tract  may be PHI, we currently don't have the governance to take
>approach 1.
>
> Welcome any input from other sites.
>
>--
>Ticket URL:
>k.org_trac_Project_ticket_544-23comment-3A15=DwICaQ=yHlS04HhBraes5BQ9u
>eu5zKhE7rtNXt_d012z2PA6ws=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE=
>wjt2QT-caC0BaQoqA-1jzlQgfOhmfVhDcHV0oV9o_sA=SiG0BJXb-ag0DCYa_svdEDeEWNVO
>JVkGOkV0JtvXSAY= > gpc-informatics
>k.org_=DwICaQ=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=CqPxCu-Eyw
>A2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE=wjt2QT-caC0BaQoqA-1jzlQgfOhmfVhDcHV0oV
>9o_sA=Mpnaed_RgiVlMRfvyIbhydJzr6UR3yEq9-l7Cbir8co= > Greater Plains
>Network - Informatics




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Medical Center



The future of medicine, today.


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RE: [gpc-informatics] #544: how to convert ACS raw variables to CAP variables (e.g. type of health insurance)?

2017-07-17 Thread Bernard Black
But it's a five-year average.
We can rely on Census not to release PHI . . .

Bernie
*
Bernard S. Black
bbl...@northwestern.edu
Nicholas D. Chabraja Professor, Northwestern University
 Pritzker School of Law
 Institute for Policy Research
 Kellogg School of Management, Finance Dep't
Law School:  375 East Chicago Ave., Chicago IL 60611
Kellogg:  2211 Campus Drive, Evanston IL 60208
tel:  law:  312-503-2784; Kellogg:  847-491-5049; cell: 847-807-9599
papers on SSRN at:  http://ssrn.com/author=16042



-Original Message-
From: Dan Connelly 
Sent: Monday, July 17, 2017 1:29 PM
To: Bernard Black ; gpc-dev@listserv.kumc.edu; 
Mei Liu ; furmanc...@icnanotox.org; kosin...@mcw.edu
Cc: btay...@mcw.edu; vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook 
; Charon Gladfelter 
; Brennan Connolly ; 
nicholas-c-sm...@uiowa.edu; phillip.ree...@utsouthwestern.edu; 
mo...@health.missouri.edu; danh...@regenstrief.org; Hillary Sandoval 
; George Kowalski 
Subject: RE: [gpc-informatics] #544: how to convert ACS raw variables to CAP 
variables (e.g. type of health insurance)?

The tract identifier identifies a geographic location with less than 20,000 
people in it, in most cases. That puts it on the PHI side of the "Safe Harbor" 
method, no?

Excerpt from "Guidance Regarding Methods for De-identification of Protected 
Health Information in Accordance with the Health Insurance Portability and 
Accountability Act (HIPAA) Privacy Rule"
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.hhs.gov_hipaa_for-2Dprofessionals_privacy_special-2Dtopics_de-2Didentification_index.html=DwIF-g=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=UogPJ7VYoAeiC8NNwyY5AxLx8QgaRiMcicgAv7oi3tc=U78KtNME0I70ZozrDQ4Eb2iFWMXFlV6L5ANpuzQvQ10=5L4-CYK_x0znYIze381codm7XjhTBwzr-NgWIiDYWfw=
  :

 the "Safe Harbor" method:
(2)(i) The following identifiers of the individual or of relatives, employers, 
or household members of the individual, are removed:
(B) All geographic subdivisions smaller than a state, including street address, 
city, county, precinct, ZIP code, and their equivalent geocodes, except for the 
initial three digits of the ZIP code if, according to the current publicly 
available data from the Bureau of the Census:
(1) The geographic unit formed by combining all ZIP codes with the same three 
initial digits contains more than 20,000 people; and
(2) The initial three digits of a ZIP code for all such geographic units 
containing 20,000 or fewer people is changed to 000

--
Dan


From: Bernard Black [bbl...@kellogg.northwestern.edu]
Sent: Monday, July 17, 2017 1:09 PM
To: gpc-dev@listserv.kumc.edu; Dan Connolly; Mei Liu; furmanc...@icnanotox.org; 
kosin...@mcw.edu
Cc: btay...@mcw.edu; vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook; Charon 
Gladfelter; Brennan Connolly; nicholas-c-sm...@uiowa.edu; 
phillip.ree...@utsouthwestern.edu; mo...@health.missouri.edu; 
danh...@regenstrief.org; Hillary Sandoval; George Kowalski
Subject: RE: [gpc-informatics] #544: how to convert ACS raw variables to CAP 
variables (e.g. type of health insurance)?

Census tract information *is* averaged, and is not PHI.
That is why Census is willing to release it.

Bernie
*
Bernard S. Black
bbl...@northwestern.edu
Nicholas D. Chabraja Professor, Northwestern University
 Pritzker School of Law
 Institute for Policy Research
 Kellogg School of Management, Finance Dep't Law School:  375 East Chicago 
Ave., Chicago IL 60611
Kellogg:  2211 Campus Drive, Evanston IL 60208
tel:  law:  312-503-2784; Kellogg:  847-491-5049; cell: 847-807-9599 papers on 
SSRN at:  
https://urldefense.proofpoint.com/v2/url?u=http-3A__ssrn.com_author-3D16042=DwIF-g=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=UogPJ7VYoAeiC8NNwyY5AxLx8QgaRiMcicgAv7oi3tc=U78KtNME0I70ZozrDQ4Eb2iFWMXFlV6L5ANpuzQvQ10=KBr07Xe7ZOUTPiBff46YgGD4jsS9d4Z74Y252zmRqRY=


-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Monday, July 17, 2017 12:11 PM
To: Dan Connelly ; mei...@kumc.edu; 
furmanc...@icnanotox.org; kosin...@mcw.edu
Cc: btay...@mcw.edu; Bernard Black ; 
vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook 
; Charon Gladfelter 
; bconno...@kumc.edu; 
nicholas-c-sm...@uiowa.edu; phillip.ree...@utsouthwestern.edu; 
mo...@health.missouri.edu; danh...@regenstrief.org; hsando...@kumc.edu; George 
Kowalski 
Subject: Re: [gpc-informatics] #544: how to convert ACS raw variables to CAP 

RE: [gpc-informatics] #544: how to convert ACS raw variables to CAP variables (e.g. type of health insurance)?

2017-07-17 Thread Mei Liu
Based on my limited understanding, ACS variables linked to a census tract 
contain aggregate/average information. But the census tract ID itself when 
linked to a patient record is PHI because it identifies a geographic location 
with <20,000 people. Am I interpreting this correctly?

Mei

-Original Message-
From: Bernard Black [mailto:bbl...@kellogg.northwestern.edu] 
Sent: Monday, July 17, 2017 1:09 PM
To: gpc-dev@listserv.kumc.edu; Dan Connolly; Mei Liu; furmanc...@icnanotox.org; 
kosin...@mcw.edu
Cc: btay...@mcw.edu; vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook; Charon 
Gladfelter; Brennan Connolly; nicholas-c-sm...@uiowa.edu; 
phillip.ree...@utsouthwestern.edu; mo...@health.missouri.edu; 
danh...@regenstrief.org; Hillary Sandoval; George Kowalski
Subject: RE: [gpc-informatics] #544: how to convert ACS raw variables to CAP 
variables (e.g. type of health insurance)?

Census tract information *is* averaged, and is not PHI.
That is why Census is willing to release it.

Bernie
*
Bernard S. Black
bbl...@northwestern.edu
Nicholas D. Chabraja Professor, Northwestern University
 Pritzker School of Law
 Institute for Policy Research
 Kellogg School of Management, Finance Dep’t Law School:  375 East Chicago 
Ave., Chicago IL 60611
Kellogg:  2211 Campus Drive, Evanston IL 60208
tel:  law:  312-503-2784; Kellogg:  847-491-5049; cell: 847-807-9599 papers on 
SSRN at:  http://ssrn.com/author=16042


-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Monday, July 17, 2017 12:11 PM
To: Dan Connelly ; mei...@kumc.edu; 
furmanc...@icnanotox.org; kosin...@mcw.edu
Cc: btay...@mcw.edu; Bernard Black ; 
vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook 
; Charon Gladfelter 
; bconno...@kumc.edu; 
nicholas-c-sm...@uiowa.edu; phillip.ree...@utsouthwestern.edu; 
mo...@health.missouri.edu; danh...@regenstrief.org; hsando...@kumc.edu; George 
Kowalski 
Subject: Re: [gpc-informatics] #544: how to convert ACS raw variables to CAP 
variables (e.g. type of health insurance)?

#544: how to convert ACS raw variables to CAP variables (e.g. type of health 
insurance)?
--+---
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  design-issue  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-stds |  Resolution:
 Keywords:|  Blocked By:
 Blocking:  598   |
--+---

Comment (by meiliu):

 Our most recent IRB protocol is in the attachment.
 - As noted in the protocol, "...variables such as income, educational  
attainment, likelihood of employment, poverty status, owner-occupied house  
value, and health insurance coverage derived from geocoded address data  will 
be used only as average values, not tied to any specific individual  but rather 
to study populations."
 - I did not find any language on sharing census tract information.
 I've discussed this with Tamara McMahon and agree that since census tract  may 
be PHI, we currently don't have the governance to take approach 1.

 Welcome any input from other sites.

--
Ticket URL: 
 gpc-informatics 
 Greater Plains Network - Informatics
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gpc-dev 18 Jul agenda and meeting notes (incl. next-d geocoding #544)

2017-07-17 Thread Dan Connolly
What else for tomorrow?

  *   gpc-dev 18 July 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)

*   #622 
PCORNet CDM Cycle 2 Refresh 2 experience report - 
CMH

 *   Next Meeting:  25 July. scribe: ???

*   Note LRU scribe schedule in 
#12

  2.  #478 (ADAPTABLE monitoring) 
reopened:
 “Query 2 will be distributed to all the sites on 08/07/2017. We(KUMC) offered 
to be a beta tester site for the Query 2. Query was shared with KUMC on 
07/14/2017. Maren Wennberg from KUMC will be working on it.”

  3.  #596 targeted 
cancer therapy study feasibility 
queries due 18 July

 *   Nicholas: will submit UIOWA’s data on query 3 and send an update out 
to the group. Done:
DROC Breast Cancer CRG Request 
(#596)   Smith, 
Nicholas C

 *   Re - in LOINC: Nick to make an adjustment for Query 3 on site specific 
factor 15  and repair the LOINC issue.

 *   Jim: Will put revised query 3 on the ticket. (OBE?)

 *   Query 1, 2, 3:

*   UNMC - “I am forwarding all three data queries to Nick.” - Campbell 
Fri 12:47:47
“Thanks for forwarding it, Jim” Smith Fri 12:51 PM

*   MCRF - “I submitted results from Marshfield based on ...” Verhagen 
Thu Jul 13 17:17:02
“No this [missing LOINC] is not a problem.” -Smith Fri 11:34:15

*   UTSW - “Query 1,2,& 3 have been uploaded by UTSW.” -- Reeder Mon 
13:03:29

*   MU: “if that [replaced 560 with 380] works then there is no need 
for me to re-run them, cause that is the data you have” - McNeely Fri 13:42:55

*   WISC -

*   KUMC -

*   MCW -

*   UMN -

  4.  
Milestone:cdm-cycle3
 due July 31

 *   #549 (discharge info disconnected from parts of some EI visits) closed 
fixed

 *   #589 
principal diagnosis 10% threshold in PCORNet 
CDM news from IU?

 *   #579 Data 
Characterization - Cycle 3 
Tracking

  5.  Milestone:cohort-char1
#570: 
collect expanded obesity cohort data 
comment:43:

 *   MCW done July 14 (comment:47)

 *   UIOWA ETA? Brian will talk this through with Mike Bingham on 7/25

  6.  Milestone:gpc-phase2-h4
#408
 collect Enrollment numbers for interim report (milestone 
2.3.5) in progress

  7.  
Milestone:next-d

 *   #544 how 
to convert ACS raw variables to CAP variables (e.g. type of health insurance)?
Attachment 
GeocodingOptionsForGPC-2017_06_27-bb.docx
 added

*   Approach 1. Add Census tract information to EHR data
“we currently don't have the governance to take approach 1”

*   Approach 2. Link health data to geocoded variables

   

RE: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 2, 3

2017-07-17 Thread Chrischilles, Elizabeth A
I believe other sites are finding this also.  It is okay if you don't find 
LOINC codes in the LABS table.  That tells us something and it's probably due 
to only a few labs being prioritized for the CDM initially.

-Original Message-
From: GPC Informatics [mailto:d...@madmode.com] 
Sent: Thursday, July 13, 2017 5:17 PM
To: dconno...@kumc.edu; Sravani Chandaka ; McDowell, 
Bradley D ; rwait...@kumc.edu; Campbell, James R 
; McClay, James C ; btay...@mcw.edu; 
mcneele...@health.missouri.edu; verhagen.lau...@marshfieldresearch.org 
; tmcma...@kumc.edu; danh...@regenstrief.org
Cc: Smith, Nicholas C ; Chrischilles, Elizabeth A 
; phillip.ree...@utsouthwestern.edu; 
gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 
2, 3

#596: targeted cancer therapy study - Query 1, 2, 3
--+
 Reporter:  dconnolly |   Owner:  schandaka
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+

Comment (by lv):

 I submitted results from Marshfield based on what Nick sent on Tuesday;  
however, within our data, we only found a few labs coded to LOINC:
 48676-1. These tests were all dated 1998, and we dropped for the CDM based  on 
the 1/1/2010 constraint.

 Is it problem to have no lab data for this? Are there other LOINC codes we  
could add?

--
Ticket URL: 

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RE: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 2, 3

2017-07-17 Thread Chrischilles, Elizabeth A
I believe this is referring to 'Central Sequence Number' and, yes, based on 
prior tumor registry data pulls, some sites had to substitute 'Hospital 
Sequence Number'.  Typically one or the other, but not both, are populated.

-Original Message-
From: McNeeley, Todd Alexander [mailto:mcneele...@health.missouri.edu] 
Sent: Friday, July 14, 2017 1:43 PM
To: gpc-dev@listserv.kumc.edu; dconno...@kumc.edu; Sravani Chandaka 
; McDowell, Bradley D ; 
rwait...@kumc.edu; Campbell, James R ; McClay, James C 
; btay...@mcw.edu; verhagen.lau...@marshfieldresearch.org 
; tmcma...@kumc.edu; 
danh...@regenstrief.org; Smith, Nicholas C 
Cc: Chrischilles, Elizabeth A ; 
phillip.ree...@utsouthwestern.edu
Subject: RE: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 
2, 3

I actually did remove the 560 and had replaced it with 380 that someone had 
suggested. So if that works then there is no need for me to re-run them, cause 
that is the data you have. 

Todd McNeeley
Programmer, Information Management Team Development 
mcneele...@health.missouri.edu  | 573-884-3297 direct | 573-219-8341 mobile 
Tiger Institute for Health Innovation | www.tiger-institute.org  PLEASE 
CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS EMAIL

-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Friday, July 14, 2017 11:23 AM
To: dconno...@kumc.edu; schand...@kumc.edu; bradley-mcdow...@uiowa.edu; 
rwait...@kumc.edu; campb...@unmc.edu; jmcc...@unmc.edu; btay...@mcw.edu; 
McNeeley, Todd Alexander ; 
verhagen.lau...@mcrf.mfldclin.edu; tmcma...@kumc.edu; danh...@regenstrief.org; 
nicholas-c-sm...@uiowa.edu
Cc: e-chrischil...@uiowa.edu; phillip.ree...@utsouthwestern.edu; 
gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 
2, 3

#596: targeted cancer therapy study - Query 1, 2, 3
--+
 Reporter:  dconnolly |   Owner:  schandaka
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+

Comment (by nsmith):

 Hello, Todd:

 The purpose of that filter in the query is to identify patients who only  have 
one primary tumor.  That was me just being thorough.  If you are  unable to 
utilize that filter on NAACCR 560, don't worry about it.  Please  remove it and 
run the queries again.  Since a high percentage of patients  in our registries 
have only had one tumor, removing this filter is not a  deal breaker.  I just 
need to make a note of which sites had this  limitation and were unable to use 
NAACCR 560 in their queries.  I know  KUMC also had a similar issue around this 
filter as well and had to remove  it.

 Todd, please remove that filter and re-run queries 2 & 3.  Please contact  me 
directly via phone or email if you any further issues or questions.

 Thanks!

 Nick

 Nicholas C. Smith, MS
 Senior Database Architect
 Institute for Clinical & Translational Science (http://www.icts.uiowa.edu)
 Email:  nicholas-c-sm...@uiowa.edu
 Phone:  319-467-8173



 Replying to [comment:25 tmcneeley]:
 > We are unable to complete Query 2 and 3 at MU because it does a join on  
 > NAACCR|560%. We do not have any people coded with 560 so the inner join  
 > returns 0 results.

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RE: [gpc-informatics] #544: how to convert ACS raw variables to CAP variables (e.g. type of health insurance)?

2017-07-17 Thread Dan Connolly
The tract identifier identifies a geographic location with less than 20,000 
people in it, in most cases. That puts it on the PHI side of the "Safe Harbor" 
method, no?

Excerpt from "Guidance Regarding Methods for De-identification of Protected 
Health Information in Accordance with the Health Insurance Portability and 
Accountability Act (HIPAA) Privacy Rule"
https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html
 :

 the “Safe Harbor” method:
(2)(i) The following identifiers of the individual or of relatives, employers, 
or household members of the individual, are removed:
(B) All geographic subdivisions smaller than a state, including street address, 
city, county, precinct, ZIP code, and their equivalent geocodes, except for the 
initial three digits of the ZIP code if, according to the current publicly 
available data from the Bureau of the Census:
(1) The geographic unit formed by combining all ZIP codes with the same three 
initial digits contains more than 20,000 people; and
(2) The initial three digits of a ZIP code for all such geographic units 
containing 20,000 or fewer people is changed to 000

-- 
Dan


From: Bernard Black [bbl...@kellogg.northwestern.edu]
Sent: Monday, July 17, 2017 1:09 PM
To: gpc-dev@listserv.kumc.edu; Dan Connolly; Mei Liu; furmanc...@icnanotox.org; 
kosin...@mcw.edu
Cc: btay...@mcw.edu; vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook; Charon 
Gladfelter; Brennan Connolly; nicholas-c-sm...@uiowa.edu; 
phillip.ree...@utsouthwestern.edu; mo...@health.missouri.edu; 
danh...@regenstrief.org; Hillary Sandoval; George Kowalski
Subject: RE: [gpc-informatics] #544: how to convert ACS raw variables to CAP 
variables (e.g. type of health insurance)?

Census tract information *is* averaged, and is not PHI.
That is why Census is willing to release it.

Bernie
*
Bernard S. Black
bbl...@northwestern.edu
Nicholas D. Chabraja Professor, Northwestern University
 Pritzker School of Law
 Institute for Policy Research
 Kellogg School of Management, Finance Dep’t
Law School:  375 East Chicago Ave., Chicago IL 60611
Kellogg:  2211 Campus Drive, Evanston IL 60208
tel:  law:  312-503-2784; Kellogg:  847-491-5049; cell: 847-807-9599
papers on SSRN at:  http://ssrn.com/author=16042


-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Monday, July 17, 2017 12:11 PM
To: Dan Connelly ; mei...@kumc.edu; 
furmanc...@icnanotox.org; kosin...@mcw.edu
Cc: btay...@mcw.edu; Bernard Black ; 
vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook 
; Charon Gladfelter 
; bconno...@kumc.edu; 
nicholas-c-sm...@uiowa.edu; phillip.ree...@utsouthwestern.edu; 
mo...@health.missouri.edu; danh...@regenstrief.org; hsando...@kumc.edu; George 
Kowalski 
Subject: Re: [gpc-informatics] #544: how to convert ACS raw variables to CAP 
variables (e.g. type of health insurance)?

#544: how to convert ACS raw variables to CAP variables (e.g. type of health 
insurance)?
--+---
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  design-issue  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-stds |  Resolution:
 Keywords:|  Blocked By:
 Blocking:  598   |
--+---

Comment (by meiliu):

 Our most recent IRB protocol is in the attachment.
 - As noted in the protocol, "...variables such as income, educational  
attainment, likelihood of employment, poverty status, owner-occupied house  
value, and health insurance coverage derived from geocoded address data  will 
be used only as average values, not tied to any specific individual  but rather 
to study populations."
 - I did not find any language on sharing census tract information.
 I've discussed this with Tamara McMahon and agree that since census tract  may 
be PHI, we currently don't have the governance to take approach 1.

 Welcome any input from other sites.

--
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 gpc-informatics 
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___

RE: [gpc-informatics] #544: how to convert ACS raw variables to CAP variables (e.g. type of health insurance)?

2017-07-17 Thread Bernard Black
Census tract information *is* averaged, and is not PHI.
That is why Census is willing to release it.

Bernie
*
Bernard S. Black
bbl...@northwestern.edu
Nicholas D. Chabraja Professor, Northwestern University
 Pritzker School of Law
 Institute for Policy Research
 Kellogg School of Management, Finance Dep’t
Law School:  375 East Chicago Ave., Chicago IL 60611
Kellogg:  2211 Campus Drive, Evanston IL 60208
tel:  law:  312-503-2784; Kellogg:  847-491-5049; cell: 847-807-9599
papers on SSRN at:  http://ssrn.com/author=16042


-Original Message-
From: GPC Informatics [mailto:d...@madmode.com] 
Sent: Monday, July 17, 2017 12:11 PM
To: Dan Connelly ; mei...@kumc.edu; 
furmanc...@icnanotox.org; kosin...@mcw.edu
Cc: btay...@mcw.edu; Bernard Black ; 
vanri...@umn.edu; meye0...@umn.edu; Lindsey Cook 
; Charon Gladfelter 
; bconno...@kumc.edu; 
nicholas-c-sm...@uiowa.edu; phillip.ree...@utsouthwestern.edu; 
mo...@health.missouri.edu; danh...@regenstrief.org; hsando...@kumc.edu; George 
Kowalski 
Subject: Re: [gpc-informatics] #544: how to convert ACS raw variables to CAP 
variables (e.g. type of health insurance)?

#544: how to convert ACS raw variables to CAP variables (e.g. type of health 
insurance)?
--+---
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  design-issue  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-stds |  Resolution:
 Keywords:|  Blocked By:
 Blocking:  598   |
--+---

Comment (by meiliu):

 Our most recent IRB protocol is in the attachment.
 - As noted in the protocol, "...variables such as income, educational  
attainment, likelihood of employment, poverty status, owner-occupied house  
value, and health insurance coverage derived from geocoded address data  will 
be used only as average values, not tied to any specific individual  but rather 
to study populations."
 - I did not find any language on sharing census tract information.
 I've discussed this with Tamara McMahon and agree that since census tract  may 
be PHI, we currently don't have the governance to take approach 1.

 Welcome any input from other sites.

--
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Re: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 2, 3

2017-07-17 Thread Phillip Reeder
Query 1,2,& 3 have been uploaded by UTSW.

Phillip

On 7/11/17, 12:06 PM, "GPC Informatics"  wrote:

>#596: targeted cancer therapy study - Query 1, 2, 3
>--+
> Reporter:  dconnolly |   Owner:  schandaka
> Type:  task  |  Status:  assigned
> Priority:  major |   Milestone:  gpc-phase2-h4
>Component:  data-sharing  |  Resolution:
> Keywords:  all-sites |  Blocked By:
> Blocking:|
>--+
>
>Comment (by campbell):
>
> We completed and uploaded Query3 results to RedCap.  We had none of the
> labs, a few medication events and lots of procedures to report.  I
> butchered Iowa's query due to differences in syntax and structure of
> OBSERVATION_FACT for NAACCR...we have KU data structures.  I ran the SQL
>I
> uploaded to this ticket in file UNMC_Oracle_Query3 and formatted the data
> by hand to fit Iowa's requirement which was easy in a spreadsheet.
>
>--
>Ticket URL:
>
>gpc-informatics 
>Greater Plains Network - Informatics




UT Southwestern


Medical Center



The future of medicine, today.


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Re: [gpc-informatics] #478: ADAPTABLE monitoring

2017-07-17 Thread GPC Informatics
#478: ADAPTABLE monitoring
--+
 Reporter:  schandaka |   Owner:  schandaka
 Type:  enhancement   |  Status:  closed
 Priority:  major |   Milestone:  adaptable-monitor
Component:  data-sharing  |  Resolution:  fixed
 Keywords:|  Blocked By:  274, 476, 496
 Blocking:|
--+

Comment (by schandaka):

 Update 07/14/2017:
 Query 2 will be distributed to all the sites on 08/07/2017. We(KUMC)
 offered to be a beta tester site for the Query 2. Query was shared with
 KUMC on 07/14/2017. Maren Wennberg from KUMC will be working on it. More
 updates to follow after KUMC's preliminary run.

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RE: [External] Re: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 2, 3

2017-07-17 Thread Smith, Nicholas C
Thanks for forwarding it, Jim.  I'll take a look and get it loaded.  Right off 
the bat the values of '10', '20', and '30' should have a preceding '0' in front 
of them.  I'll see what's going on with the other values.

Nick




Nicholas C. Smith, MS
Senior Database Architect
Institute for Clinical & Translational Science (http://www.icts.uiowa.edu)
Email:  nicholas-c-sm...@uiowa.edu
Phone:  319-467-8173




-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Friday, July 14, 2017 12:48 PM
To: dconno...@kumc.edu; schand...@kumc.edu; McDowell, Bradley D; 
rwait...@kumc.edu; campb...@unmc.edu; jmcc...@unmc.edu; btay...@mcw.edu; 
mcneele...@health.missouri.edu; verhagen.lau...@mcrf.mfldclin.edu; 
tmcma...@kumc.edu; danh...@regenstrief.org; Smith, Nicholas C
Cc: Chrischilles, Elizabeth A; phillip.ree...@utsouthwestern.edu; 
gpc-dev@listserv.kumc.edu
Subject: [External] Re: [gpc-informatics] #596: targeted cancer therapy study - 
Query 1, 2, 3

#596: targeted cancer therapy study - Query 1, 2, 3
--+
 Reporter:  dconnolly |   Owner:  schandaka
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+

Comment (by campbell):

 I tried several times to reload Query3 and corrected several minor  formatting 
issues but ran up against data formatting restrictions.  It  would not accept 
'BLANK', '10', '20', '30' for ssf15 or CPT_HCPCS code of  'G0461' or G0462'.  I 
am forwarding all three data queries to Nick.

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Re: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 2, 3

2017-07-17 Thread GPC Informatics
#596: targeted cancer therapy study - Query 1, 2, 3
--+
 Reporter:  dconnolly |   Owner:  schandaka
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+

Comment (by nsmith):

 Hi, Jim:

 Regarding Query 3...

 That explains why the data was missing from UNMC.  I have made the request
 to Tamara to modify the Query 3 project status from "development" to
 "production".  Tamara has just made the update to production.  Please give
 Query 3 upload another try.

 Regarding Query 1...

 For just UNMC, if you could simply email me your Query 1 template data I
 will merge it on my end here at UIOWA.  That way I can quickly get Betsy
 the accurate Query 1 numbers.

 Thanks, Jim.

 Nick

 Nicholas C. Smith, MS
 Senior Database Architect
 Institute for Clinical & Translational Science (http://www.icts.uiowa.edu)
 Email:  nicholas-c-sm...@uiowa.edu
 Phone:  319-467-8173


 Replying to [comment:33 campbell]:
 > I loaded Query3 results before changes to the file structure to allow
 SSF15 and my records were trashed when the file structure was changed.
 Now when I go to load, I have the message "This project is in development
 status and real data should not be loaded.
 >
 > I made an error loading Query1 results and did not assign unique
 record_id with the result that RedCap is miscounting the totals of tumor
 cases and tells me I only have 278 records out of the 1300+ I loaded.
 >
 > Can I get my Query1 project reset so I can load with proper record_ids?
 I would appreciate a production status for my Query3 project and a wipe of
 data so I can load Query3 results.
 > Jim Campbell

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Re: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 2, 3

2017-07-17 Thread GPC Informatics
#596: targeted cancer therapy study - Query 1, 2, 3
--+
 Reporter:  dconnolly |   Owner:  schandaka
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+

Comment (by campbell):

 I tried several times to reload Query3 and corrected several minor
 formatting issues but ran up against data formatting restrictions.  It
 would not accept 'BLANK', '10', '20', '30' for ssf15 or CPT_HCPCS code of
 'G0461' or G0462'.  I am forwarding all three data queries to Nick.

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RE: [External] RE: DROC Breast Cancer CRG Request (#596)

2017-07-17 Thread Smith, Nicholas C
Hello, Jim:

I marked this down in the ticket #596 today but figured I would email you as 
well.  Please give the Query 3 upload another try today.  If you still have 
issues please just email me your Query 3 template with your data and I'll see 
what I can do.

Thanks!

Nick


[cid:image002.jpg@01D2FC9B.8EB54320]

Nicholas C. Smith, MS
Senior Database Architect
Institute for Clinical & Translational Science 
(http://www.icts.uiowa.edu)
Email:  nicholas-c-sm...@uiowa.edu
Phone:  319-467-8173



From: Campbell, James R [mailto:campb...@unmc.edu]
Sent: Wednesday, July 12, 2017 6:43 AM
To: Smith, Nicholas C; gpc-dev@listserv.kumc.edu
Subject: [External] RE: DROC Breast Cancer CRG Request (#596)

Nicholas
So I reformatted our data to include SSF15 and tried to reload the spreadsheet 
but I no longer have  access to the Data Import Tool probably because I did it 
already and then you changed file format.  Please reset Query3 status so I can 
import or I can forward directly to you to manage
Jim Campbell

From: Gpc-dev [mailto:gpc-dev-boun...@listserv.kumc.elet me know and I will 
forward spreadsheet to you for you to manage.
Jim Campbelldu] On Behalf Of Smith, Nicholas C
Sent: Tuesday, July 11, 2017 3:50 PM
To: gpc-dev@listserv.kumc.edu
Subject: DROC Breast Cancer CRG Request (#596)

Hello, Everyone:

I believe a couple of sites had stated on the dev call today that they were 
able to upload their Query3 results into Redcap.  But as of about 30 minutes 
ago I had not seen any results uploaded to the Query3 project.

I was able to upload UIOWA's results into the "Cancer CRG DROC Query3" project 
this afternoon.  I originally left out the SSF15 field from the Query 3 Redcap 
project.  I have since added it in.  The following links on 
(#596) have been 
updated to reflect those changes...

Query #3 Template
https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/596/CancerCRGDROCQuery3_ImportTemplate_2017-06-12.csv

Query #3 Template Example
https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/596/CancerCRGDROCQuery3_ImportTemplate_(example).csv

DROC Breast Cancer Queries Power Point
https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/596/DROC%20Breast%20Cancer%20Queries.pptx

So if you have not started Query #3 please use these updated materials for help!

Also, please feel free to contact me regarding any portion of this request.  I 
am more than happy to assist.  Just let me know.

My contact information is below.

Thanks!

[cid:image003.jpg@01D2FC9B.8EB54320]

Nicholas C. Smith, MS
Senior Database Architect
Institute for Clinical & Translational Science 
(http://www.icts.uiowa.edu)
Email:  nicholas-c-sm...@uiowa.edu
Phone:  319-467-8173



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Re: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 2, 3

2017-07-17 Thread GPC Informatics
#596: targeted cancer therapy study - Query 1, 2, 3
--+
 Reporter:  dconnolly |   Owner:  schandaka
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+

Comment (by nsmith):

 Hello, Laurel:

 No this is not a problem.  I think Betsy may have mentioned this in the
 past, but part of this exercise is to see what we have in our CDMs
 ''now''.  We realized going into this that most sites only mapped LOINC
 codes for the top 80-90% of the most utilized labs and that these specific
 LOINC codes listed in the DROC probably would not fall into that category.
 UIOWA also experienced this and had no LOINC codes returned in Query 3.
 For Query 3 just submit what you were able to find of the
 CPT/NDC/RXCUI/LOINC listed in the DROC/PowerPoint, nothing more, nothing
 less.

 Does that help?

 Also, feel free to contact me with any further questions.

 Nick

 Nicholas C. Smith, MS
 Senior Database Architect
 Institute for Clinical & Translational Science (http://www.icts.uiowa.edu)
 Email:  nicholas-c-sm...@uiowa.edu
 Phone:  319-467-8173


 Replying to [comment:32 lv]:
 > I submitted results from Marshfield based on what Nick sent on Tuesday;
 however, within our data, we only found a few labs coded to LOINC:
 48676-1. These tests were all dated 1998, and we dropped for the CDM based
 on the 1/1/2010 constraint.
 >
 > Is it problem to have no lab data for this? Are there other LOINC codes
 we could add?

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RE: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 2, 3

2017-07-17 Thread McNeeley, Todd Alexander
I actually did remove the 560 and had replaced it with 380 that someone had 
suggested. So if that works then there is no need for me to re-run them, cause 
that is the data you have. 

Todd McNeeley
Programmer, Information Management Team Development
mcneele...@health.missouri.edu  | 573-884-3297 direct | 573-219-8341 mobile  
Tiger Institute for Health Innovation | www.tiger-institute.org
 PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS EMAIL

-Original Message-
From: GPC Informatics [mailto:d...@madmode.com] 
Sent: Friday, July 14, 2017 11:23 AM
To: dconno...@kumc.edu; schand...@kumc.edu; bradley-mcdow...@uiowa.edu; 
rwait...@kumc.edu; campb...@unmc.edu; jmcc...@unmc.edu; btay...@mcw.edu; 
McNeeley, Todd Alexander ; 
verhagen.lau...@mcrf.mfldclin.edu; tmcma...@kumc.edu; danh...@regenstrief.org; 
nicholas-c-sm...@uiowa.edu
Cc: e-chrischil...@uiowa.edu; phillip.ree...@utsouthwestern.edu; 
gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #596: targeted cancer therapy study - Query 1, 
2, 3

#596: targeted cancer therapy study - Query 1, 2, 3
--+
 Reporter:  dconnolly |   Owner:  schandaka
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  gpc-phase2-h4
Component:  data-sharing  |  Resolution:
 Keywords:  all-sites |  Blocked By:
 Blocking:|
--+

Comment (by nsmith):

 Hello, Todd:

 The purpose of that filter in the query is to identify patients who only  have 
one primary tumor.  That was me just being thorough.  If you are  unable to 
utilize that filter on NAACCR 560, don't worry about it.  Please  remove it and 
run the queries again.  Since a high percentage of patients  in our registries 
have only had one tumor, removing this filter is not a  deal breaker.  I just 
need to make a note of which sites had this  limitation and were unable to use 
NAACCR 560 in their queries.  I know  KUMC also had a similar issue around this 
filter as well and had to remove  it.

 Todd, please remove that filter and re-run queries 2 & 3.  Please contact  me 
directly via phone or email if you any further issues or questions.

 Thanks!

 Nick

 Nicholas C. Smith, MS
 Senior Database Architect
 Institute for Clinical & Translational Science (http://www.icts.uiowa.edu)
 Email:  nicholas-c-sm...@uiowa.edu
 Phone:  319-467-8173



 Replying to [comment:25 tmcneeley]:
 > We are unable to complete Query 2 and 3 at MU because it does a join on  
 > NAACCR|560%. We do not have any people coded with 560 so the inner join  
 > returns 0 results.

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