RE: PROD_P02_DQA_FDPRO_DIAQ_NSD6_r001 SAS query

[Bos, Angela]

On the dev call today, it was mentioned that we should use the SITE_IDs as 
shown in ticket #384 attachment: Data Strategy 
Meeting.pdf.
 The pdf includes a note saying "Please start using site numbers and names in 
all correspondence with the coordinating center!" However the "DataMart 
Description" given in the pdf is longer than the available field size of 
DATAMART_NAME in the CDM HARVEST table, so we will have to use something 
different in the CDM table.

UTHSCSA may need to talk to the coordinating center about changing our official 
PCORnet information, because both our site ID and description indicate that we 
are UTSA, which a different institution. Our full institution name is better, 
but also not correct in this pdf, and the university is picky about these 
things.

For the reasons above, we are using this in the HARVEST table:
datamart_id=C4UTHSCSA
datamart_name=C4-GPC-UTHSCSA
network_id=C4
network_name=GPC

-Angela

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Michael Prittie
Sent: Monday, March 14, 2016 3:48 PM
To: Kowalski, George; 
Subject: Re: PROD_P02_DQA_FDPRO_DIAQ_NSD6_r001 SAS query

Hi George,
The CDMv3 spec says the following 
(ref):

NETWORKID - This identifier is assigned by DSSNI operations
NETWORK_NAME - Descriptive name of the network
DATAMARTID - This identifier is assigned by DSSNI operations
DATAMART_NAME - Descriptive name of the datamart

Our network id is GPC and our datamart id is KUMC.  I believe the associated 
name fields would then be Greater Plains Collaborative and University of Kansas 
Medical Center respectively.

Best,
Michael Prittie
Biomedical Informatics Software Engineer
Division of Medical Informatics
University of Kansas Medical Center





From: 
> 
on behalf of "Kowalski, George" >
Date: Monday, March 14, 2016 at 2:53 PM
To: ">" 
>
Subject: PROD_P02_DQA_FDPRO_DIAQ_NSD6_r001 SAS query

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
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RE: PCORnet Diagnostic Query - UIOWA, WISC, CMH

[Bos, Angela]

Hi Laurel,

UTHSCSA received the SAS diagnostic query request yesterday. But I see that we 
were not slated for the Feb 8th query request. Does the Feb 22nd deadline apply 
to us?

-Angela | UTHSCSA


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Verhagen, Laurel A
Sent: Tuesday, February 02, 2016 2:34 PM
To: prakash-nadka...@uiowa.edu; Thomas F Mish  (m...@wisc.edu); 
Wanta Keith M (kwa...@uwhealth.org); Fothergill, Rita, R (rfotherg...@cmh.edu); 
wcteach...@cmh.edu
Cc: gpc-dev@listserv.kumc.edu; Greenlee, Robert T PHD
Subject: PCORnet Diagnostic Query - UIOWA, WISC, CMH

Hi everyone,

DRN OC continues to roll out the SAS Diagnostic Query, which requires PCORnet 
CDM v3, based on SAS readiness dates collected in November. (This query is 
available on Central Desktop/iMeet Central and linked from ticket 
#374.)

The next three sites selected from GPC include: UIOWA, WISC, CMH.

The deadline to return the diagnostic query will be around 2/22 (2 weeks) 
according to Dr. Louzao.

Please let me know if your site is ready to receive the SAS query. If your site 
is not ready, please provide your revised SAS readiness date. Let me know if 
you have any questions.

Thanks,
Laurel

From: Darcy Louzao, Ph.D. [mailto:darcy.lou...@duke.edu]
Sent: Tuesday, February 02, 2016 1:14 PM
To: Greenlee, Robert T PHD; Verhagen, Laurel A
Cc: James Topping; Laura Qualls
Subject: PCORnet Diagnostic Query

Good afternoon,
Based on the SAS readiness dates you provided in late 2015, we plan to send the 
Diagnostic Query next Monday, February 8th to the following data partners. 
Please let us know if you are not ready and would like to revise your dates 
accordingly.

C4 GPC (University of Iowa)

C4 GPC (UW Madison)

C4 GPC (Children's Mercy)


Thank you,
Darcy


Darcy M. Louzao Ph.D.
Project Leader
Duke Clinical Research Institute
ph: 919-668-8017 | cell: 336-255-3231

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RE: How long do other sites leave the Height/Health REDCap survey active?

[Bos, Angela]

The survey is officially closed. You may deactivate your surveys in REDCap 
after you have submitted your survey data per ticket 
#379.


Angela Bos
Clinical Informatics Research Division
Department of Epidemiology and Biostatistics
UT Health Science Center at San Antonio
Phone: (210) 562-4074

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Swander, Lena C
Sent: Wednesday, January 06, 2016 11:56 AM
To: Verhagen, Laurel A; Brittany Zschoche; 'Thomas Mish'; 
gpc-dev@listserv.kumc.edu
Cc: SARAH L ESMOND; Kolk Daniel A
Subject: Re: How long do other sites leave the Height/Health REDCap survey 
active?


At Iowa, our survey is also still active.  Our first and only mailing went out 
to 5016 individuals on 10/6/15. To date, our last respondent completed the 
survey on 12/29. Our de-dentified data was uploaded to the GPC REDCap on 1/4/15.



If UTHSCSA would like us to de-activate the survey at this point, please let us 
know.



Thanks!

-Lena

Project Coordinator | Institute for Clinical and Translational Science
MPH Candidate 2016 | Department of Epidemiology
College of Public Health, University of Iowa
Office Phone: 319-384-9936



From: 
gpc-dev-boun...@listserv.kumc.edu 
> 
on behalf of Verhagen, Laurel A 
>
Sent: Wednesday, January 6, 2016 9:20 AM
To: Brittany Zschoche; 'Thomas Mish'; 
gpc-dev@listserv.kumc.edu
Cc: SARAH L ESMOND; Kolk Daniel A
Subject: RE: How long do other sites leave the Height/Health REDCap survey 
active?


At Marshfield, we've left our survey active. Just checked and we've received 
one response (12/4) since exporting de-identified survey data for UTHSCSA. Our 
final email invite was sent on 10/20, and the previous last response was 
received on 11/19.



Thanks,
Laurel



From: 
gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Brittany Zschoche
Sent: Wednesday, January 06, 2016 9:08 AM
To: 'Thomas Mish'; gpc-dev@listserv.kumc.edu
Cc: SARAH L ESMOND; Kolk Daniel A
Subject: RE: How long do other sites leave the Height/Health REDCap survey 
active?



Tom,



I asked Sarah Schlachter and she made note to mention it on the next obesity 
call, Wednesday, 1/13.



Until then, would welcome updates/input from other sites.



Thanks,



Brittany



From: 
gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Thomas Mish
Sent: Wednesday, January 06, 2016 9:01 AM
To: gpc-dev@listserv.kumc.edu
Cc: SARAH L ESMOND >; Kolk Daniel A 
>
Subject: How long do other sites leave the Height/Health REDCap survey active?



All,



I don't recall this conversation and or language talking about this issue, but 
I was curious how long each of our sites have left the H/W REDCap survey active 
after sending out the invitation. We didn't send our out until recently 
(mid-December) and are still getting a handful (2-10) every day yet. Plotting 
response rates seems to leave me in doubt that this will ever tail off 
completely but I'm assuming that eventually we'll reach a point of diminishing 
returns. Do other sites still have their REDCap surveys active? If not, at what 
point did you deactivate the survey?



-TM
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Obesity survey data collection

[Bos, Angela]

On the gpc-dev call tomorrow, UTHSCSA would like to review and receive comments 
on the following plans for collecting the obesity survey results. For reference:

#379: Link EHR data to Health and Medical Research Family Survey (HMRFS) 2 
results
#404: How to export and collect non-identifying fields from the HMRFS REDCap 
survey?

We assume that local study coordinators will probably bear responsibility for 
verifying completeness and de-identification of survey data, and gpc-dev teams 
may assist with exporting/uploading to GPC-REDCap. Because the breakdown of 
work may differ across sites, we are supporting this effort on both the gpc-dev 
call/listserv and the regular weight/height call/listserv.

Goals:
1)  To collect all data in GPC-REDCap by early December (except UW Madison, 
hopefully by end of Dec)
2)  To ensure all data uploaded to GPC-REDCap is de-identified

Each site should do the following:
1)  Make sure all responses, bounce backs, etc. are recorded in REDCap 
project "tracker form"
2)  Review & edit data dictionary to ensure tracker form fields containing 
HIPAA identifiers are 
flagged as such. At UTHSCSA we had to add
a.  pat_age
b.  mailaddress2
3)  Make sure the identifier flag is removed from the following tracker 
form field
a.  patient_num - this should be a de-identified patient number needed to 
link extracted EMR data (SQLite data builder files)
4)  Eyeball data in tracker form text fields to ensure no HIPAA 
identifiers are included
a.  At a minimum check these fields:
i.  contact_type
ii. match_type
iii.first_con_atmpt_res
iv. survey_contact_method
v.  survey_contact_person
vi. comment_1
vii.comment_2
viii.   comment_3
b.  Example: at UTHSCSA, during survey tracking we sometimes stored phone 
numbers in comment_1 & comment_2, so we marked them as identifiers in the data 
dictionary
5)  Make sure any changes to the REDCap data dictionary to mark identifier 
fields are promoted from draft mode into production
6)  Export raw data
a.  Project Home > Export Data
b.  On the row "All data (all records and fields)", click the "Export Data" 
button
c.  Select CSV / Microsoft Excel (raw data)
d.  Check the box to "Remove all tagged Identified fields"
e.  Check the box to "Export survey identifier field and survey timestamp 
field(s)"
f.  Click the "Export Data" button, and save the file
g.  Review it for missing essentials or present identifiers. We recommend 
using several reviewers please. Clean up as necessary.
h.  Upload this file to the GPC-REDCap project: "Weight/Health Survey Data 
Federation", form: "REDCap Data Raw"
7)  Export data dictionary - this is needed to interpret the raw data as 
sites may have made localizations
a.  Project Setup, scroll down to the bottom of the page and click "Data 
Dictionary" button
b.  Click the link to "Download the current Data Dictionary"
c.  Upload this file to the GPC-REDCap project: "Weight/Health Survey Data 
Federation", form: "REDCap Data Dictionary"

Outstanding Issues:
1)  Does the age of survey respondent, which was voluntarily collected as 
part of the survey protocol, constitute PHI? If so, can we still collect this 
as a limited data set?

For assistance, questions, and comments, please contact:
  David Rupert
  Data System Coordinator, Pediatrics-Endocrinology
  Email: rupe...@uthscsa.edu
  Phone: 210-567-5283


Angela Bos
Clinical Informatics Research Division
Department of Epidemiology and Biostatistics
UT Health Science Center at San Antonio
Phone: (210) 562-4074



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RE: [gpc-informatics] #12: Teleconference records for gpc-dev weekly - 7/14/2015

[Bos, Angela]

Additionally, here is a link to the GPC obesity survey readiness 
tablehttps://docs.google.com/spreadsheets/d/1GSFgxGDjJHxPAUwv0KnHCJpebSR8cjtYFrvJXMuxxvU/edit?usp=sharing.
 New columns have been added since we polled the sites last week. You should 
have edit access to fill in missing any data for your site.

-Angela


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, July 20, 2015 11:12 AM
To: Thomas Mish; gpc-dev@listserv.kumc.edu
Subject: RE: [gpc-informatics] #12: Teleconference records for gpc-dev weekly - 
7/14/2015

Thanks, Tom.

full text attached for the archive.

--
Dan

From: 
gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu 
[gpc-dev-boun...@listserv.kumc.edu] on behalf of Thomas Mish [m...@wisc.edu]
Sent: Wednesday, July 15, 2015 10:51 AM
To: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: FW: [gpc-informatics] #12: Teleconference records for gpc-dev weekly - 
7/14/2015

The link to yesterday's 
minuteshttps://docs.google.com/document/d/1DR1MSa752O5yT8lnGvkTiUVwzcZVnYTKVneN1FjxVhQ/edit?usp=sharing
 can be found as a part of ticket 
#12https://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:70.



-TM





-Original Message-
From: GPC Informatics [mailto:d...@madmode.com]
Sent: Wednesday, July 15, 2015 8:35 AM
To: dconno...@kumc.edumailto:dconno...@kumc.edu; 
jd...@umn.edumailto:jd...@umn.edu; ngra...@kumc.edumailto:ngra...@kumc.edu; 
verhagen.lau...@mcrf.mfldclin.edumailto:verhagen.lau...@mcrf.mfldclin.edu; 
huhick...@nebraskamed.commailto:huhick...@nebraskamed.com; 
bo...@uthscsa.edumailto:bo...@uthscsa.edu; 
b...@uthscsa.edumailto:b...@uthscsa.edu; Thomas Mish
Subject: Re: [gpc-informatics] #12: Teleconference records for gpc-dev weekly



#12: Teleconference records for gpc-dev weekly

---+---

Reporter:  dconnolly  |   Owner:  jdale

 Type:  task   |  Status:  assigned

Priority:  minor  |   Milestone:

Component:  data-stds  |  Resolution:

Keywords: |  Blocked By:

Blocking: |

---+---



Comment (by mish):



UTSW has volunteered for the 21st. Thanks Debbie/Angela for the combined  
efforts on the notes for this meeting.



*

[https://docs.google.com/document/d/1DR1MSa752O5yT8lnGvkTiUVwzcZVnYTKVneN1FjxVhQ/edit

gpc-dev 14-Jul 2015 google doc notes]



--

Ticket URL: 
http://informatics.gpcnetwork.org/trac/Project/ticket/12#comment:70

gpc-informatics http://informatics.gpcnetwork.org/

Greater Plains Network - Informatics
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Obesity survey tracker

[Bos, Angela]

Attention sites participating in the obesity survey,

Today we posted some updates to the obesity survey 
trackerhttps://bitbucket.org/bos_uthscsa/survey_tracker/overview. 
Specifically these changes will make handling surveys by email invitation 
easier and clearer. Instructions have also been updated to with better 
documentation about the format and required fields for the contact info input 
file. The contact info input file is optional, and should be used by sites that 
do not have Clarity/identified DW/Oracle databases. Additionally, we added a 
sample survey_tracker output file in the format used to upload the initial 
project data into REDCap.

Below is an example with more detailed info for a couple steps in the 
Instructions based on the specific needs of CMH. Because they are a non-Epic 
(Cerner) site, and also because a pediatric/email-only site, they must use the 
contact input file method.

Step 5) Configure the survey_tracker

- Create a copy of tracker.ini.example file to start, name it tracker.ini

- Set site specific settings
[site]
site_abbr=CM
adult_only=false
use_email=true

- Set your data builder SQLite and contact info file names
[input_files]
deid_db= databuilder_obesity_pediatric.db
contact_info=contact_info.csv

- delete everything below this line (or add your own known patterns to be match 
in bad address strings)
[invalid_patterns]

- leave everything else default; none of it will be used

Step 6) OPTIONAL: create preloaded contact info file in format of 
id_data_DEMO.csv

At minimum the following fields must be populated: patient_ide, patient_number, 
guardian_name, guardian_email

Step 7) Run the survey_tracker, using the -f option

$ python tracker_load.py -f
2015.07.14 19:39:21:   Creating dir: output
2015.07.14 19:39:21: contacts info file: contact_info.csv
2015.07.14 19:39:21:deid_db: databuilder_obesity_pediatric.db
2015.07.14 19:39:21: tracker_db: tracker.db
...
2015.07.14 19:39:21: adult_only: False
2015.07.14 19:39:21: email_only: True
...

Step 8) Validate your i2b2 data builder and survey_tracker SQLite files

$ python validate_databuilder.py databuilder_obesity_pediatric.db 
output/tracker.db

 Please copy-n-paste the output of this command in an email to me, or at 
least confirm that you see no errors.


Questions, comments, and feedback are welcome!

-Angela | UTHSCSA



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REDCap survey invitation email question

[Bos, Angela]

Does anyone know how to insert images into the survey invitation email on 
REDCap? If not able to insert an image directly, can a link to an image in the 
RC project file repository be used?


- Angela | UTHSCSA

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ALS REDCap feedback

[Bos, Angela]

Hi Bhargav,

UTHSCSA is working to move our ALS REDCap project to production, but we have 
some issues to resolve.

In the KUMC data 
dictionaryhttps://informatics.gpcnetwork.org/trac/Project/attachment/ticket/208/PCORIALSREDCapSurvey_DataDictionary_2015-03-23.csv,
 the following fields were not marked as identifiers, so we set it to 'Y': mrn, 
who, consent_language (participant types own name in here).

We removed the required flag for address/email fields, because we are using 
one or the other for specific participants, and we have not populated all the 
data for each of them.

We also edited piping fields in the text of Clinic Validation instrument 
field who to match the variable names from the data dictionary. Was the 
[address] piped field here supposed to refer to mailing street address or email?

This is shown at the top of the Als Clinic Survey instrument CONSENT 
LANGUAGE CONSENT LANGUAGECONSENT LANGUAGECONSENT LANGUAGECONSENT 
LANGUAGECONSENT ...

The same instrument also says: THIS IS A DRAFT VERSION. DO NOT ENTER REAL 
DATA.

In our specific REDCap ( Version 6.4.4), we cannot enable the participant 
identifier option in the Participant List. The button to enable it does not 
exist on the Participant List page as it should. Our project is in development, 
so we should not require intervention by an administrator to do this, but we 
cannot find docs on how to enable the button to enable this.

We plan to use survey_access_code instead of unique survey url. Therefore we 
will change the field on the Survey Web Access form and use it to store the 
data. Will this or any other changes we mentioned cause problems with later 
analysis of project data?

We are also having a strange issue with our record ID field in REDCap. This 
field is usually the first field in the project, so by uploading the data 
dictionary record_id is used. However, when we load the online designer to 
verify the form, the username of the person who imported the data is shown in 
the record_id field, instead of real imported data. Looking at a record of test 
data, we see the record_id populated correctly, but the MRN field shows the 
REDCap user instead of the real value. (Looking at the field history here shows 
correct value and username for last edit). This one is really odd, and we might 
have to involve our RC administrator to resolve it.


-Angela

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RE: maternal, sibling linkage for antibiotic obesity study?

[Bos, Angela]

For the purposes of the pediatric obesity survey, we wanted to identify 
siblings to prevent sending multiple surveys to the same family, and having 
some false positives is OK, especially for such a large cohort. The best way of 
finding them seems to be matching by the parent/guardian phone numbers. We have 
many siblings who, for various reasons, do not share a contact name or address. 
Here’s the process with a little bit of background on how we get 
parent/guardian contact info.

We use the following order of precedence for contact names, addresses, and 
phone numbers, taking the first one where all address fields pass minimal 
validation checks:
clarity.account (billing), clarity.emergency_contacts  (mother  father  
guardian  emerg1  emerg2).

If the contact full name matches the patient full name, we assume this in an 
independent young adult, and may skip them accordingly. If the preferred 
address has no name, we send letters to Mr. or Mrs. Patient_Last_Name. If none 
of those preferred addresses are available, we use patient address and send 
letter to Mr. or Mrs. Patient_Last_Name.

To find siblings, first we compare phone valid phone numbers for matches, then 
zip codes, then we do a fuzzy match (using Levenshtein distance) on addresses 
that are formatted for comparison as follows:

- ignore city and state (using zip code only)
- concatenate street line1+line2 and upper case it
- remove periods and commas
- abbreviate directional words per USPS rules
- abbreviate street suffixes, PO boxes, and rural route types per USPS rules
- remove commonly omitted street suffixes (AVE, DR, LN, RD, ST)
- apartment, #, lot, or unit designations are formatted similarly (e.g. 
‘unit|123’)
- tokenize the string and list in the following order
   - ZIP|BOX[|RT NUM][RT TYPE]
  - e.g. PO Box 99 RR 2 Poteet, Tx 9 - ‘9|99|RR|9’
   -  ZIP|STREET NAME|STREET NUM[|UNIT|123]
  - e.g. ‘123 Main Ave # 44 San Antonio, TX 9’ - 
‘9|MAIN|123|unit|44’

We set the fuzzy match threshold higher for addresses with unit numbers. This 
would be much simpler if we had a geocoding system in place. However, as it 
turned out, in our cohort of 4220 patients, we identified 193 family groups, 
and only resorted to address matching for 28 of them. 165 were matched on phone 
numbers alone.

We also had some potential false positives for what appear to be multiple 
families living together. In other words, contacts addresses matched exactly, 
but no names or phone numbers matched. Again, for the purposes of our survey 
and limiting responses to one per family, we are OK with this.

-Angela | UTHSCSA


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Bos, Angela
Sent: Thursday, May 07, 2015 12:50 PM
To: Justin Dale; Dan Connolly
Cc: gpc-dev@listserv.kumc.edu; GPC Obesity Research Team 
(gpc-obes...@listserv.kumc.edu)
Subject: RE: maternal, sibling linkage for antibiotic obesity study?

Our preliminary checks showed we had little data in our Clarity patient 
relationship link fields.  But we have used a fuzzy matching algorithm on 
patent contact info to identify siblings, which isn’t 100% accurate and could 
use some improvement, so our answer was ‘yes’ with caveats. The basic algorithm 
will be shared with gpc-dev soon.

- Angela | UTHSCSA


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: Thursday, May 07, 2015 12:33 PM
To: Dan Connolly
Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu; GPC Obesity 
Research Team 
(gpc-obes...@listserv.kumc.edumailto:gpc-obes...@listserv.kumc.edu)
Subject: Re: maternal, sibling linkage for antibiotic obesity study?

From the Clarity data dictionary:

Table: PATIENT_2
Field: MOTHER_PAT_ID
Description: The unique ID of the system patient record belonging to the mother 
of this patient. This item is populated if the motherís record is linked to the 
patient record in enterprise registration system Registrationís emergency 
contacts. This ID may be encrypted.

Table: PATIENT_2
Field: FATHER_PAT_ID
Description: The unique ID of the system patient record belonging to the father 
of this patient. This item is populated if the fatherís record is linked to the 
patient record in enterprise registration system Registrationís emergency 
contacts. This ID may be encrypted.



Justin

On Thu, May 7, 2015 at 12:19 PM, Dan Connolly 
dconno...@kumc.edumailto:dconno...@kumc.edu wrote:
Do you know how we get these from CLARITY?

--
Dan

From: Campbell, James R [campb...@unmc.edumailto:campb...@unmc.edu]
Sent: Thursday, May 07, 2015 11:59 AM
To: Dan Connolly; gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu; 
GPC Obesity Research Team 
(gpc-obes...@listserv.kumc.edumailto:gpc-obes...@listserv.kumc.edu)
Subject: RE: maternal, sibling linkage for antibiotic obesity study?
Simple links between

RE: maternal, sibling linkage for antibiotic obesity study?

[Bos, Angela]

Our preliminary checks showed we had little data in our Clarity patient 
relationship link fields.  But we have used a fuzzy matching algorithm on 
patent contact info to identify siblings, which isn’t 100% accurate and could 
use some improvement, so our answer was ‘yes’ with caveats. The basic algorithm 
will be shared with gpc-dev soon.

- Angela | UTHSCSA


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Justin Dale
Sent: Thursday, May 07, 2015 12:33 PM
To: Dan Connolly
Cc: gpc-dev@listserv.kumc.edu; GPC Obesity Research Team 
(gpc-obes...@listserv.kumc.edu)
Subject: Re: maternal, sibling linkage for antibiotic obesity study?

From the Clarity data dictionary:

Table: PATIENT_2
Field: MOTHER_PAT_ID
Description: The unique ID of the system patient record belonging to the mother 
of this patient. This item is populated if the motherís record is linked to the 
patient record in enterprise registration system Registrationís emergency 
contacts. This ID may be encrypted.

Table: PATIENT_2
Field: FATHER_PAT_ID
Description: The unique ID of the system patient record belonging to the father 
of this patient. This item is populated if the fatherís record is linked to the 
patient record in enterprise registration system Registrationís emergency 
contacts. This ID may be encrypted.



Justin

On Thu, May 7, 2015 at 12:19 PM, Dan Connolly 
dconno...@kumc.edumailto:dconno...@kumc.edu wrote:
Do you know how we get these from CLARITY?

--
Dan

From: Campbell, James R [campb...@unmc.edumailto:campb...@unmc.edu]
Sent: Thursday, May 07, 2015 11:59 AM
To: Dan Connolly; gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu; 
GPC Obesity Research Team 
(gpc-obes...@listserv.kumc.edumailto:gpc-obes...@listserv.kumc.edu)
Subject: RE: maternal, sibling linkage for antibiotic obesity study?
Simple links between record IDs of parents and family member could be 
maintained as social history observations using clinical observation codes in 
i2b2:

Identity of mother LOINC 74025-8
Identity of father LOINC 74026-6
Identity of family member  LOINC 74024-1

LOINC also has a substantial number of observables relating to data about the 
mother and child:
Maternal education  57712-2
Maternal pregnancies  75201-4
Maternal marital status 75257-6


James R. Campbell MD
campb...@unmc.edumailto:campb...@unmc.edu
Office 402-559-7505tel:402-559-7505
Secretary 402-559-7299tel:402-559-7299
Fax 402-559-8396tel:402-559-8396
Pager 402-888-1230tel:402-888-1230

From: 
gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu]
 On Behalf Of Dan Connolly
Sent: Thursday, May 07, 2015 8:55 AM
To: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: maternal, sibling linkage for antibiotic obesity study?

Question 4 of the antibiotic survey 
(#277https://informatics.gpcnetwork.org/trac/Project/ticket/277) asks about 
maternal and sibling links. We have an issue in this area, 
#103https://informatics.gpcnetwork.org/trac/Project/ticket/103, but we closed 
it as wontfix. Did any of you answer yes to 4a/b/c? If so, we should perhaps 
re-open #103.

--
Dan

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RE: [gpc-informatics] #281: performance of Q1 QA query on non-Neteeza systems

[Bos, Angela]

I think it took about 30 min on single instance Oracle 12c here, definitely a 
matter of minutes not hours. 

UTHSCSA QA query v6 
https://bitbucket.org/njgraham/pcori-qa/src/7ce69cfb8f37/Q1_2015_Quality_Query_v6.sql?at=uthscsa

Which is a modified version from this branch
https://bitbucket.org/njgraham/pcori-qa/branch/oracle_v6

-Angela

-Original Message-
From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Tom Mish
Sent: Tuesday, April 28, 2015 8:00 AM
To: gpc-dev@listserv.kumc.edu
Subject: Re: [gpc-informatics] #281: performance of Q1 QA query on non-Neteeza 
systems

Besides KUMC, did anyone else happen to note how long the query took to run at 
each site? I'd especially love to hear from MCW with their postges site.

-TM


On 4/28/2015 7:50 AM, GPC Informatics wrote:
 #281: performance of Q1 QA query on non-Neteeza systems
 --+
   Reporter:  mish  |   Owner:  mish
   Type:  problem   |  Status:  new
   Priority:  minor |   Milestone:  data-quality3
 Component:  data-sharing  |  Resolution:
   Keywords:|  Blocked By:
   Blocking:|
 --+
 Description changed by mish:

 Old description:

 cf 21 Apr discussion (#12)

 ''Dan, reporting for Tom, who will presumably elaborate the 
 description in due course.''
 New description:

   Nathan Graham reports run time of over 17 hours on an Oracle system that
   took only 15-20 minutes to complete on Netezza. Other users anecdotally
   reported long times as well.

   It should be runnable on: Oracle, Netezza, postgres, and MS SQL systems. I
   suspect that solving the problem for Oracle solves it for most systems.

 --

 --
 Ticket URL: 
 http://informatics.gpcnetwork.org/trac/Project/ticket/281#comment:1
 gpc-informatics http://informatics.gpcnetwork.org/
 Greater Plains Network - Informatics

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RE: GPC-Dev Agenda 4-21

[Bos, Angela]

Sorry for the late request, but could we add the following topic for the 
obesity survey:

What version of Redcap are you running? How soon could your site potentially 
achieve 6.1.x?

We would like to use Redcap “access code” functionality introduced in 6.1.0. 
Used in conjunction with participant lists, it allows a user to enter a general 
survey URL, then requires them to enter a non-case-sensitive 9-character access 
code to go to their unique survey link.

-Angela | UTHSCSA


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Monday, April 20, 2015 3:30 PM
To: Apathy,Nate; gpc-dev@listserv.kumc.edu
Subject: RE: GPC-Dev Agenda 4-21

Thanks for getting the ball rolling, Nate. I went over our business and made 
some adjustments.

Note in particular that I dropped items where I couldn't find an update shared 
with the group.  Reminder: if anyone wants something on the agenda, please send 
mail or update a ticket before 10am Monday. You can, of course, ask to have 
something added when we review the agenda at the beginning of the call, but 
things work better if materials are available in advance.



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

a.​Meeting ID and access code: 
817-393-381https://global.gotomeeting.com/meeting/join/817393381; call +1 
(571) 317-3131

b.roll: all 10 
DevTeamshttps://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams 
represented?

  i.KUMC, CMH, UIOWA, WISC, MCW, 
MCRF, UMN, UNMC, UTHSCSA, UTSW, (MU), (IU)

ii.Reminder - put institution after 
your name on the GoToMeeting (preferences)

c.meeting notes 
(#12https://informatics.gpcnetwork.org/trac/Project/ticket/12): previous 
notes OK? today's scribe: Nate A (Cerner/CMH) comments on the agenda? chair 
dropped items where no update was available as of ~T-24hrs

   .recent tickets opened/closed 
FYI:

1.#165:https://informatics.gpcnetwork.org/trac/Project/ticket/165 
PopMedNet @ UTSW - closed

2.#270http://informatics.gpcnetwork.org/trac/Project/ticket/270 - Port Q1 
QA query to Oracle opened

3.note also recent ticket comments 
reporthttps://informatics.gpcnetwork.org/trac/Project/report/13

d.Next Meeting April 28th: scribe?

2.#78 Shared GPC RxNORM/NDFRT medications 
ontologyhttps://informatics.gpcnetwork.org/trac/Project/ticket/78 re-opened; 
also #236https://informatics.gpcnetwork.org/trac/Project/ticket/236

.  Nate sent list of non-SCDF 
codeshttp://listserv.kumc.edu/pipermail/gpc-dev/2015q2/001525.html to group

3.#158 Usable LOINC Labs - March 27 
commenthttps://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:28 
proposes that  Jan 19 
detailshttps://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:20 
suffice

.  KUMC’s experience is positive so far, though we haven’t released

a.is what’s on babel consistent with Jan 19 details?

4.
milestone:data-quality3https://informatics.gpcnetwork.org/trac/Project/milestone/data-quality3

.  #270 (Port Q1 QA query to Oracle) 
closedhttps://informatics.gpcnetwork.org/trac/Project/ticket/270#comment:2

5.milestone:bc-survey-cohort-def 
(depgraphhttps://informatics.gpcnetwork.org/trac/Project/depgraph/ticket/227):

.  #271https://informatics.gpcnetwork.org/trac/Project/ticket/271 IRB-wait

a.#264https://informatics.gpcnetwork.org/trac/Project/ticket/264 confirm 
governance and workflow: ~7 sites responded

6.Milestone: 
obesity-survey-defhttps://informatics.gpcnetwork.org/trac/Project/milestone/obesity-survey-def

.  #252 test results from 
wischttps://informatics.gpcnetwork.org/trac/Project/ticket/252#comment:5

7.
milestone:cohort-char1https://informatics.gpcnetwork.org/trac/Project/milestone/cohort-char1

.  #258https://informatics.gpcnetwork.org/trac/Project/ticket/258 
volunteer to take a whack at breast cancer treatment from NAACCR?

8.#242https://informatics.gpcnetwork.org/trac/Project/ticket/242 - Nate 
A. asks Apr 16 “where can we find the necessary attachments and code to attempt 
this? ...”

  1.  milestone:data-domains3 currently has no due date; is that OK? are there 
any customers waiting?


--
Dan

From: 
gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu 
[gpc-dev-boun...@listserv.kumc.edu] on behalf of Apathy,Nate 
[nate.apa...@cerner.com]
Sent: Monday, April 20, 2015 9:50 AM
To: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: GPC-Dev Agenda 4-21
Hi all - I’ve started the agenda/notes 
dochttps://docs.google.com/document/d/1W0zFvJwC0S20vzumCI-roRNoo2ux-M6uJNx2o7E4TrY/edit?usp=sharing
 for tomorrow’s dev call and everyone should have access to edit. Much of the 
agenda below is follow-up from last week. Let me know if there are specific 
items to include on this agenda 

Medication Modifiers

[Bos, Angela]

Phillip, can you be more specific on how you populated the RX|CURRENT 
medication modifier? Sample code would be great. Looking at the Hackathon2  
notes

NateA: What does current Meds mean?
Phillip: anything that was included on the encounter.


Thanks!
Angela Bos | UTHSCSA


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Hackathon II survey, need job title for secure wi-fi

[Bos, Angela]

The field Job Title has been added to the Hackathon II survey. This field is 
required by UTHSCSA to permit secure wi-fi access.

Please update your survey if you have already responded, or fill it out if you 
haven't done so yet.

https://redcap.uthscsa.edu/REDCap/surveys/?s=qcLVmeAfzt

Thanks!

Angela Bos
Clinical Informatics Research Division
Department of Epidemiology and Biostatistics
UT Health Science Center at San Antonio
Phone: (210) 562-4074



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RE: vital status from EMR for breast cancer cohort characterization (#67, #32, #204)

[Bos, Angela]

We at San Antonio would be interested in sharing. We have a process similar to 
what Philip described where our EMR and tumor registry teams report deaths to 
each other on a monthly basis, but the systems are never truly in sync. Updates 
on each side are from various sources and not done on a regular basis. We would 
greatly benefit from a more authoritative source for this information.


Angela Bos
Clinical Informatics Research Division
Department of Epidemiology and Biostatistics
UT Health Science Center at San Antonio
Phone: (210) 562-4074

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Russ Waitman
Sent: Monday, December 15, 2014 3:37 PM
To: 'Phillip Reeder'; Tamara McMahon; Dan Connolly
Cc: Steve Fennel; gpc-dev@listserv.kumc.edu
Subject: RE: vital status from EMR for breast cancer cohort characterization 
(#67, #32, #204)

We might think about whether we at KUMC might sign the paperwork with NIST so 
we can distribute our SSA files to other GPC partners as part of our existing 
agreement.
http://www.ntis.gov/products/ssa-dmf/#http://www.ntis.gov/products/ssa-dmf/

There used to be a signification $5000+ charge associated with acting as a 
distributor but it seems since the changes in the interim rule
http://www.gpo.gov/fdsys/pkg/FR-2014-03-26/pdf/2014-06701.pdf
, that may be gone.
http://www.ntis.gov/assets/pdf/ssdmf-raw%20data%20form.pdf

We want to check though that we are complying with the proper protocols with 
use of the file. Clearly enhancing trial recruitment and research for PCORI 
should be in scope.

Do we think enough places would want to use our feed?

Russ

From: 
gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Phillip Reeder
Sent: Monday, December 15, 2014 1:57 PM
To: Tamara McMahon; Dan Connolly
Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: Re: vital status from EMR for breast cancer cohort characterization 
(#67, #32, #204)

I would definitely check the EMR vital status in addition to the tumor registry 
vital status.  If you have both loaded into i2b2,  it's very easy to do a query 
to find how many patients are alive in one source, but deceased in the other.  
For our tumor registry,  I typically run that report every few months and send 
it to the tumor registry group so they can update their database.  Since both 
data sources(Tumor Registry and EMR) get death information from different 
sources, they will always have some variation.

Phillip


From: Tamara McMahon tmcma...@kumc.edumailto:tmcma...@kumc.edu
Date: Monday, December 15, 2014 at 1:44 PM
To: Dan Connolly dconno...@kumc.edumailto:dconno...@kumc.edu
Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu 
gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: RE: vital status from EMR for breast cancer cohort characterization 
(#67, #32, #204)

Dan,

For HERON, I plan to use Deceased and Deceased per SSA.  Vital status, 
especially deceased, is needed for the BC survey so it can be excluded from the 
survey population.  Nobody wants to send/receive a survey to a deceased 
patient.  I am not sure about the ALS and Obesity surveys, but I am guessing 
they will want to exclude deceased from their searches as well.

Tamara

From: Dan Connolly
Sent: Monday, December 15, 2014 11:36 AM
To: Tamara McMahon
Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: vital status from EMR for breast cancer cohort characterization (#67, 
#32, #204)

Tamara, have you picked out a term for vital status from the EMR for #204?

I hear that the breast cancer survey work might want to use not just tumor 
registry data but also vital status from the EMR.

So I went to check on the status of this data element in GPC, and I suppose it 
falls into the demographics issue 
(#67https://informatics.gpcnetwork.org/trac/Project/ticket/67) though I'm not 
sure whether that's been explicit yet; the focus has been:


  *   Demographics

 *   Age
 *   Gender
 *   Race
 *   Ethnicity
Then I looked to see where it is in the PCORNet CDM, and I found... it's not. 
There's no vital status nor date of death. The closest I found is Discharged 
alive vs Expired in ENCOUNTER.DISCHARGE_STATUS.

--
Dan




UT Southwestern Medical Center
The future of medicine, today.
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RE: how to preserve saved queries on i2b2 refresh?

[Bos, Angela]

Yes, we asked, and this is a very helpful write up and set of links. Thanks!

-Angela

From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Thursday, December 04, 2014 4:58 PM
To: Wanta Keith M; gpc-dev@listserv.kumc.edu
Subject: RE: how to preserve saved queries on i2b2 refresh?

The short answer, for HERON at KUMC, is:

  *   Saved queries are supported indefinitely.

 *   We mostly try to evolve terminologies gracefully,

*   but sometimes we don't bother and we let queries with those terms 
break.

  *   Saved patient sets are supported for 3 months.

To elaborate on the honest broker and version control conversation...

i2b2 stores both queries and patient sets. How to preserve them across 
refreshes? Essentially, back up and restore the relevant tables and schemas 
(PM, QT, workplace). For (some) details, see 
HeronLoad#Productioncut-overhttps://informatics.kumc.edu/work/wiki/HeronLoad#Productioncut-over.

Do patient ids change? yes; we regenerate them every month, which invalidates 
any saved patient sets.

This was rude to users who would build a patient set on the 30th, only to find 
it's horked the next day. Our approach to this honest broker issue is: we 
update patient sets, filling in the corresponding new patient_nums, but only 
for three months; if we did it indefinitely, then the patient_num could serve 
as a long-term patient identifier, largely defeating of its privacy 
protections. (for reference: ticket #699, July 2013 sappa 
releasehttps://informatics.kumc.edu/work/blog/heron-sappa-update)

And yes, there's a lot to talk about w.r.t. ontology version control; we have a 
dozen or so tickets tagged 
terminology-evolutionhttps://informatics.kumc.edu/work/query?keywords=%7Eterminology-evolutioncol=idcol=summarycol=keywordscol=statuscol=ownercol=typecol=priorityorder=priority
 (only about half published :-/).

If a user re-runs a query and the terminology has changed so that some of the 
query's terms are no longer there, it fails (with no clue to the user what's 
going on, either :-/). So in cases such as 
#1955https://informatics.kumc.edu/work/ticket/1955 where our notes tree had a 
clumsy extra ROOT node...

Choices include:

  *   Get rid of it

 *   Let any existing queries that use terms below it in the hierarchy 
break.
 *   Preserve old queries by maintaining a hidden tree (as for old 
diagnosis terms in #441 and 
source:heron_load/concepts_merge.sql#L278https://informatics.kumc.edu/work/browser/heron_load/concepts_merge.sql#L278
 )

  *   Keep it

In that case, ... we decided not to worry about preserving old queries, 
whereas when we refined our diagnosis terms, we did keep the old terms, but 
with c_visualattributes set to hide them.



p.s. I didn't ask the question; I think the question was from Angela or Alex in 
San Antonio. I just brought it here for discussion from the meeting notes.

--
Dan

From: Wanta Keith M [kwa...@uwhealth.org]
Sent: Tuesday, December 02, 2014 6:27 PM
To: Dan Connolly; gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: RE: how to preserve saved queries on i2b2 refresh?
Very good question Dan!

UW Madison currently disables old queries on each i2b2 refresh if our concepts 
change.  So we just do it for each release for now to be safe.  We are not 
handling patient ids (or any ids) correctly yet after a refresh.  This is an 
ice breaker for a great honest broker and ontology version control conversation.

From: 
gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Dan Connolly
Sent: Tuesday, December 02, 2014 1:48 PM
To: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: how to preserve saved queries on i2b2 refresh?

I didn't notice this question in today's meeting notes:


*  Question: on re-deploy to i2b2, how to preserve saved queries? Do patient 
IDs, etc change. Does i2b2 re-run saved queries or use stored patient sets with 
old ids?



Here's hoping for time to answer... or maybe Nathan will beat me to it.

grumble. We have extensive internal documentation on this issue; I wish I could 
just point you to it.

--
Dan
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RE: GPC Lab Tree Construction Methodology

[Bos, Angela]

AT UTHSCSA our labs currently shown in babel are not correctly mapped from EPIC 
component IDs. Rather than curate the lab data into categories, we're working 
on a UMLS meta-thesaurus LOINC implementation, which should be deployed soon.


Angela Bos
Clinical Informatics Research Division
Department of Epidemiology and Biostatistics
UT Health Science Center at San Antonio
Phone: (210) 562-4074


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Belay Demeke
Sent: Thursday, November 13, 2014 1:53 PM
To: 'gpc-dev@listserv.kumc.edu'
Subject: GPC Lab Tree Construction Methodology


Hello All,



Looking at the i2b2 Laboratory Test hierarchy construction, it appeared that 
many sites use different methodologies. For instance, KUMC is built based on 
EMR, UMNC based on Regenstrief Institute's LOINC tree, UMN based on UMLS, and 
MCRF based on Harvard(LLB22/i2b2/SHRINE).



Our goal is to find out which  tree construction methodology is used for the 
following  sites -  MCW, CMH, UIowa, UTSW, UTHSCA and WISC. Can you please send 
us your feedback what methodology used at your site?



Thank you,

Belay Demeke

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RE: GPC Lab Tree Construction Methodology

[Bos, Angela]

At UTHSCSA, our preliminary findings seem to show that we get 98% mapping of 
Clarity component IDs to LOINC using either UMLS meta-thesaurus or UNMC terms 
(from PCORnet loincv3_unmc_export.csv).

-Angela


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Campbell, James R
Sent: Thursday, November 13, 2014 7:11 PM
To: Thomas F Mish; gpc-dev@listserv.kumc.edu
Cc: Campbell, Walter S
Subject: RE: GPC Lab Tree Construction Methodology


We are preparing a more pragmatically oriented (lab departments and orderables) 
lab LOINC that is pruned to represent only those lab tests reported in our 
system.  If we could get sets of LOINC codes actually reported from all GPC 
sites, we would be glad to create the union of the sets and then organize 
around a clinically friendly view of lab LOINC

Jim


From: 
gpc-dev-boun...@listserv.kumc.edumailto:gpc-dev-boun...@listserv.kumc.edu 
[gpc-dev-boun...@listserv.kumc.edu] on behalf of Thomas F Mish [m...@wisc.edu]
Sent: Thursday, November 13, 2014 3:27 PM
To: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: Re: GPC Lab Tree Construction Methodology
WISC started with what simply came out of the raw EPIC system (lab components 
with LOINC when available).

-TM

On 11/13/2014 1:52 PM, Belay Demeke wrote:

Hello All,



Looking at the i2b2 Laboratory Test hierarchy construction, it appeared that 
many sites use different methodologies. For instance, KUMC is built based on 
EMR, UMNC based on Regenstrief Institute's LOINC tree, UMN based on UMLS, and 
MCRF based on Harvard(LLB22/i2b2/SHRINE).



Our goal is to find out which  tree construction methodology is used for the 
following  sites -  MCW, CMH, UIowa, UTSW, UTHSCA and WISC. Can you please send 
us your feedback what methodology used at your site?



Thank you,

Belay Demeke




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RE: Agenda for the gpc-dev call today from Jim McClay

[Bos, Angela]

Started the agenda google doc

https://docs.google.com/document/d/1i6gXeOHTo_hy8scgN_qeqtCu2KnghTXHU6mrdS-r8lM/edit?usp=sharing


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Nathan Graham
Sent: Tuesday, November 04, 2014 10:39 AM
To: GPC-DEV@LISTSERV.KUMC.EDU
Subject: Agenda for the gpc-dev call today from Jim McClay

All,

Here is the agenda for the call gpc-dev call today that Jim McClay sent out Tue 
11/4/2014 8:43 AM.  gpc-devhttp://listserv.kumc.edu/pipermail/gpc-dev/ wasn't 
in the copy list, but I think it's reasonably clear based on the e-mail 
discussion that he intended for it to be distributed to the group.

 1)Patient Generated Information according to PCORI
 2)Our proposal to PCORI dated 7-9-14
 3)Survey of network capabilities
 4)Next steps.

 Link to PCORI PRO Task Force Slides 
 https://pcornet.centraldesktop.com/taskforces/file/31721898/
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RE: parseable spreadsheet version of CDM 2.x?

[Bos, Angela]

Thanks, Bonnie. Here are some initial thoughts by UTHSCSA using your feedback 
template on CDM v2 (including a few questions on CDM v1 fields).


Angela Bos
Clinical Informatics Research Division
Department of Epidemiology and Biostatistics
UT Health Science Center at San Antonio
Phone: (210) 562-4074


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Bonnie Westra
Sent: Friday, October 24, 2014 7:32 AM
To: Dan Connolly
Cc: gpc-dev@listserv.kumc.edu; PCORnet Data Standards, Security, and Network 
Infrastructure Task Force
Subject: Re: parseable spreadsheet version of CDM 2.x?

If this helps, I started filling out the template for UMN to respond.  It may 
not have the detail you want but feel free to use if it is helpful

Bonnie L. Westra, PhD, RN, FAAN, FACMI
Associate Professor, University of Minnesota,
School of Nursing  Institute for Health Informatics
Director, Center for Nursing Informatics
Location - WDH 6-155
P - 612-625-4470, Fax - 612-625-7091
email - westr...@umn.edumailto:westr...@umn.edu
Mail - WDH 5-140, 308 Harvard St SE, Minneapolis, MN 55455



On Thu, Oct 23, 2014 at 12:16 PM, Dan Connolly 
dconno...@kumc.edumailto:dconno...@kumc.edu wrote:
So you don't plan to make it available during the review period? That's 
disappointing, but I can deal.

--
Dan

From: PCORnet Data Standards, Security, and Network Infrastructure Task Force 
[ds...@pcornet.orgmailto:ds...@pcornet.org]
Sent: Thursday, October 23, 2014 9:30 AM
To: Dan Connolly
Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
Subject: Re: parseable spreadsheet version of CDM 2.x?
Hi Dan,

Yes, there will be a CDM v2.0 parseable addendum included in the final CDM v2.0 
packet (release in late November).

Thank you,
The DSSNI TF Leadership Team


On Tue, Oct 21, 2014 at 11:34 AM, Dan Connolly 
dconno...@kumc.edumailto:dconno...@kumc.edu wrote:
The pcornet-cdm1-parseable.xlsx addendum to CDM 1.x was very useful for our 
review etc.

Should we expect something similar for CDM 2.x? An ETA would help me decide 
whether to just parse the tables in the Word doc like I originally did for 1.x.

ref: 
grokdm.pyhttps://bitbucket.org/DanC/pcornet-dm/src/197654672da365ba2ca8120458f2d57cdb7395b3/grokdm.py

--
Dan



--

The PCORnet DSSNI Task Force
ds...@pcornet.orgmailto:ds...@pcornet.org

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CDM v2 0 Draft_Feedback Template UTHSCSA.xlsx
Description: CDM v2 0 Draft_Feedback Template UTHSCSA.xlsx
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RE: Questions on KUMC's NAACCR_txform.sql

[Bos, Angela]

There is an mdb (MS Access) file you can download, see the url in the 
tumor_reg\Makefile, that contains tblCode, tblItem, tblSection, which 
correspond to the Heron t_* tables. At UTHSCSA we reverse engineered a load 
script for the t_* tables using the access ones.

-Angela Bos



From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Lenon Patrick
Sent: Monday, October 20, 2014 1:05 PM
To: 'Nathan Graham'; Dan Connolly; 'Gpc-dev@listserv.kumc.edu'
Cc: Mish Thomas F
Subject: RE: Questions on KUMC's NAACCR_txform.sql

Thx for all the info, Nate.  I'll take these to the gpc-dev list.

Dan, below there are a few questions about NAACCR/HERON that I couldn't puzzle 
out looking at your load/transform scripts, specifically: 
https://informatics.kumc.edu/work/browser/heron_load/naaccr_txform.sql

Would you mind looking at those when convenient?  Thanks.

I also have some questions about the CDM for NAACCR up on Babel, but I'll put 
them on a new thread.

From: Nathan Graham [mailto:ngra...@kumc.edu]
Sent: Monday, October 20, 2014 12:45 PM
To: Lenon Patrick; Dan Connolly
Cc: 'Kowalski, George'; Mish Thomas F
Subject: RE: Questions on KUMC's NAACCR_txform.sql

Dan, could you help with the questions below?

Patrick,

Dan Connolly is probably the most knowledgeable about NAACCR/HERON.  Also, 
perhaps we could move this conversation to the gpc-dev list?  Others might 
benefit from the conversation as well.



From: Lenon Patrick [mailto:ple...@uwhealth.org]
Sent: Friday, October 17, 2014 11:48 AM
To: Nathan Graham
Cc: 'Kowalski, George'; Mish Thomas F
Subject: Questions on KUMC's NAACCR_txform.sql

Hi Nathan,
I have a pretty good grasp of your transform proc now but I have a few nagging 
questions, please reply when convenient:


1)  You reference tables naaccr.t_item and naaccr.t_section.  I suspect 
they are just normalized tables created from the NAACCR data dictionary (see 
attached) with a separate table for the section types.  If so, did you generate 
the Section_ID field yourself?  It's the only one I don't see in NAACCR.



2)  The tumor_item_value (aka TIV) view is based on table 
naaccr_extract_eav.  The view tumor_reg_facts then merges TIV with 
naaccr.extract.  So, what's naaccr_extract_eav?  My guess is that it's a clone 
of naaccr.extract that contains properly transformed and formatted fact values. 
 If so (or if I'm even close), where does naaccr_extract_eav get loaded up and 
transformed?

If you can help me with these couple of items I'll be way ahead on this.  
Thanks for leading the way.


Patrick Lenon
HIMC Informatics Specialist
608 890 5671

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RE: PCORnet DRN - Site Contacts C4

[Bos, Angela]

UTHSCSA analyst for PopMedNet:
Angela Bos
b...@uthscsa.edumailto:b...@uthscsa.edu


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Verhagen, Laurel A
Sent: Tuesday, September 16, 2014 5:45 PM
To: gpc-dev@listserv.kumc.edu
Subject: GPC: PCORnet DRN - Site Contacts C4

After initially deferring the distributed approach, we’re coming back to 
providing the information requested below.

Please provide contact information for the individuals identified on the DEV 
call today:

CMH/Cerner: complete (Apathy, Meyer)
IOWA: add Prakash - need contact information
KUMC: add Brandon Hamlin - need contact information
MCRF: complete (Verhagen)
MCW: complete (Kowalski)
UMN: complete (Dale)
UNMC: add Mike Munns - need contact information
UTSCA: add TBD - need contact information
UTSW: complete (Morrison)
WISC: add Keith Wanta - kwa...@uwhealth.orgmailto:kwa...@uwhealth.org?

Analyst with email is required; Investigator can be skipped or included.

Thanks,
Laurel

From: PopMedNet Support [mailto:supp...@popmednet.org]
Sent: Thursday, June 12, 2014 1:30 PM
To: Greenlee, Robert T PHD; Verhagen, Laurel A
Cc: rwait...@kumc.edumailto:rwait...@kumc.edu
Subject: PCORnet DRN - Site Contacts C4 Follow Up

Dear Robert and Laurel,

We would like follow up to notify you that we have not received the contact 
information for an investigator and analyst for each of your network sites and 
the target date to do so has past. This is a necessary step in the Query Tool 
on-boarding process; a list of site contacts for every network is needed in 
order to advance. Please reply to this email with the investigator and analyst 
contacts for each site in C4 - GPC (with or without associated data, DataMart) 
no later than 6/18/2014. If you have any questions or need any additional 
information, please email 
pcornet...@popmednet.orgmailto:pcornet...@popmednet.org.
Thank you,

The PopMedNet Team


PopMedNet Team
Department of Population Medicine
Harvard Medical School  Harvard Pilgrim Health Care Institute
133 Brookline Ave., 6th Floor, Boston, MA 02215
supp...@popmednet.orgmailto:supp...@popmednet.org
www.popmednet.orghttp://www.popmednet.org|popmednet.atlassian.net/wikihttp://popmednet.atlassian.net/wiki


The contents of this message may contain private, protected and/or privileged 
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Please contact the sender and advise of the erroneous delivery by return e-mail 
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San Antonio catchment area

[Bos, Angela]

We are still in progress of determining whether UTMed clinics have an official 
catchment area.

The geography of our CTRC catchment area includes 38 counties, covering 45,970 
square miles including long distance oncology care. Counties served:

1.  Atascosa
2.  Bandera
3.  Bee
4.  Bexar
5.  Brooks
6.  Cameron
7.  Comal
8.  Dimmit
9.  Duval
10. Edwards
11. Frio
12. Gillespie
13. Guadalupe
14. Hidalgo
15. Jim Wells
16. Jim Hogg
17. Karnes
18. Kennedy
19. Kendall
20. Kerr
21. Kinney
22. Kleberg
23. La Salle
24. Live Oak
25. Maverick
26. McMullen
27. Medina
28. Nueces
29. Real
30. San Patricio
31. Starr
32. Uvalde
33. Val Verde
34. Webb
35. Willacy
36. Wilson
37. Zapata
38. Zavala


Angela Bos
Clinical Informatics Research Division
Department of Epidemiology and Biostatistics
UT Health Science Center at San Antonio
Phone: (210) 562-4074



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RE: Encounter types for ADD and PCORI CDM compliance

[Bos, Angela]

Updated spreadsheet link:
https://pcornet.centraldesktop.com/p/aQACBU-K


From: gpc-dev-boun...@listserv.kumc.edu 
[mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Bos, Angela
Sent: Tuesday, September 09, 2014 5:08 PM
To: gpc-dev@listserv.kumc.edu
Subject: Encounter types for ADD and PCORI CDM compliance

Ok, trying this again hopefully without triggering auto-encryption...

At San Antonio, we are mapping Clarity PAT_ENC.ENC_TYPE_C to the PCORI 
categories. Values  1000 are Clarity defaults, values = 1000 are local to our 
clinics.

Mapping results:

UN: (2540,2542)
IP: (2541)
OT: (3,6,7,40,50,102,105,119,151,2517,2521,2522,2523,2524,2525,2526,2539)
OA: (61,69,70,107,109,111,152,201,2101,2505,2506,2507,2516,2520,2529,2538)
AV: 
(101,106,150,1001,1200,1300,2503,2504,2508,2509,2510,2511,2512,2513,2514,2515,2519,2527,2528,2531,2532,2533,2535,2537)
NI: (null)

Details in this spreadsheet on PCORnet:
https://pcornet.centraldesktop.com/p/aQACBTRn

Any feedback will be appreciated. Thanks!


Angela Bos
Clinical Informatics Research Division
Department of Epidemiology and Biostatistics
UT Health Science Center at San Antonio
Phone: (210) 562-4074



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Encounter types for ADD and PCORI CDM compliance

[Bos, Angela]

Ok, trying this again hopefully without triggering auto-encryption...

At San Antonio, we are mapping Clarity PAT_ENC.ENC_TYPE_C to the PCORI 
categories. Values  1000 are Clarity defaults, values = 1000 are local to our 
clinics.

Mapping results:

UN: (2540,2542)
IP: (2541)
OT: (3,6,7,40,50,102,105,119,151,2517,2521,2522,2523,2524,2525,2526,2539)
OA: (61,69,70,107,109,111,152,201,2101,2505,2506,2507,2516,2520,2529,2538)
AV: 
(101,106,150,1001,1200,1300,2503,2504,2508,2509,2510,2511,2512,2513,2514,2515,2519,2527,2528,2531,2532,2533,2535,2537)
NI: (null)

Details in this spreadsheet on PCORnet:
https://pcornet.centraldesktop.com/p/aQACBTRn

Any feedback will be appreciated. Thanks!


Angela Bos
Clinical Informatics Research Division
Department of Epidemiology and Biostatistics
UT Health Science Center at San Antonio
Phone: (210) 562-4074



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ETL Annotated Data Dictionary - Data Description

[Bos, Angela]

Attached is UTHSCSA's first draft of the Data Description tab. 
Questions/comments are welcome.



Angela Bos
Clinical Informatics Research Division
Department of Epidemiology and Biostatistics
UT Health Science Center at San Antonio
Phone: (210) 562-4074



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