--
Dan
*From:* gpc-dev-boun...@listserv.kumc.edu
[gpc-dev-boun...@listserv.kumc.edu] on behalf of Alex Bokov
[bo...@uthscsa.edu]
*Sent:* Monday, October 24, 2016 3:46 PM
*To:* gpc-dev@listserv.kumc.edu
*Cc:* 'Hanrahan Larry P
If it's not too late, I would like to add these questions that came from
the Obesity paper-writing group (v2.0):
1. To do a verbal poll of each site during the call to see if who has
payer data in their i2b2
(Medicare/Medicaid/BCBS/Self-Pay/Commercial/Government/Contract/Other),
and
On 03/03/2016 09:01 AM, GPC Informatics wrote:
OK, so Jay / UNMC no longer has the ball...
He only no longer has the ball for as long as it takes me to read the
emails, and it's highly likely that he will then again have the ball.
Alex, a common pattern with all-sites tickets like this
ur amazing turnaround time.
On 02/15/2016 10:39 AM, Tamara McMahon wrote:
All,
The GPC received a feasibility request that includes a questionnaire
and multiple queries from Dr. Laura Tenner at UTHSC-SA. Queries are
located on Babel at *Shared\Medicaid Expansion* Alex Bokov is a
contact for
Just remembered, as of Hackathon3 I owe everyone the "validation script"
I wrote for DataBuilder (script attached). If you pass it to sqlite3 on
the command line, it will spit out a bunch of tables summarizing what's
in your .db file.
This is not dependent on what database you run your i2b2
Following up on Angela's comment in the rubric file...
Note: the VARIABLE table in the .db file answers the same questions
as the XML file, so if data builder is used, we do not need the XML files.
...but either way we _always_ need the VARIABLE table to exist and be
populated in the .db
At last week's gpc-dev call Hugh reported problems running DataBuilder
due to the size of the result-set and I recommended that sites with more
than 20k patients limit the eligibility dates to a more restrictive
range than in the query I sent out such that their cohort shrinks to
around 20k,
Hello. In case folks are filtering the automated ticket updates to
gpc-dev, this one is actually timely and important, so I'm bumping it
with a manual post.
People supporting the obesity survey teams at their respective sites,
please have a look at this comment...
The part of the protocol that survived numerous rounds of revision and
reality checks against what happens when actually tried in REDCap is this:
Information about which of 24 sub-cohorts that patient is in, and what
site they're at, is encoded in the first five characters in the
`proj_id`
At today's body-weight working group call, I found out that in addition
to WISC, CMH and KUMC are also planning to rely on email addresses as
the preferred channel for patient contact. Any others?
At San Antonio, the only email field in Clarity we rely on is
PATIENT.EMAIL_ADDRESS. However,
Yes, I will ask Sergio to scribe.
On 05/19/2015 12:19 PM, Dan Connolly wrote:
I neglected to recruit one.
A die roll comes up 9 - UTHSCSA, do you accept the nomination?
--
Dan
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Thanks. Who is the local lead for the obesity survey?
How many fewer patients are there in 1a. and 1b. when these criteria are
enforced vs. when they are not enforced?
Thanks again.
On 04/02/2015 04:09 PM, Debbie Yoshihara wrote:
WISC did query 1a and 1b.
Our site requires two additional
On 03/03/2015 04:05 PM, Dan Connolly wrote:
Mind if I share with the rest of gpc-dev?
Doing so now. :-)
*From:* Teresa Bosler [teresa.bos...@utsouthwestern.edu]
*Sent:* Tuesday, March 03, 2015 2:37 PM
*To:* Dan Connolly; Supreet Kathpalia
*Cc:* Bhargav Adagarla; Alex Bokov; Phillip Reeder
On 03/03/2015 04:22 PM, Bhargav Adagarla wrote:
The few things I noticed which can be implementation risks:
- The other survey plans (ALS and breast cancer) seem technically
simpler. For example, with ALS Survey (which is closest to Obesity
Survey in terms of the implementation) might not
The obesity Redcap project will have a Survey and data form for study
tracking:
* Tracker (contains invitation mail-out dates, non-automated response
status info, etc.)
o data can/will be uploaded in batch (Excel spreadsheet), e.g. to
assign a mail out date to wave X
Oh, and I had forgotten one more source of inflation (no pun intended):
If you have any visits with raw BMIs 140 recorded, those are almost
certainly artifactual, caused by using pounds instead of kilograms. I
would omit those before mapping to percentiles.
On 02/04/2015 04:01 PM, Alex
On 02/04/2015 12:43 PM, GPC Informatics wrote:
#210: Query by BMI percentile among children.
-+-
Reporter: bokov| Owner: gkowalski
Type: enhancement
UMN folks, if you have a few minutes, perhaps you'd like to join the
below conference to confirm that everything will go smoothly end-to-end
during the real Hackathon?
Our away team got a little held up heading over to the future site of
the Hackathon, but the test should begin in about 10
10:15 for 1:45: Morning Session 2
1. Breast Cancer Survey Finder File
https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonTwo#bc-finder-wp1
led by Kansas/UIOWA
2. informatics support for ALS, Obesity cohort surveys
Please note... the information for reserving a hotel room near campus
https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonTwo#CourtyardMedicalCenter
has changed slightly (thanks, Dan). The rate code is UTX, not UTXL.
They call it the Cancer Therapy Res. rate, but this event is
Hello. We're about to finalize our attendee survey for Hackathon 2 in
San Antonio.
1) What Hackathon 2 needs most is agenda items. Let's discuss those in
this conversation thread and update this page with the results:
https://informatics.gpcnetwork.org/trac/Project/wiki/HackathonTwo
Please
I'm getting KUMC's secure encrypted attachment notice when I sent the
XLS file with the updated empirical data dictionary.
There is nothing sensitive in the attachment, I don't know what
triggered this. I'm tempted to zip the file and re-send it to the list.
Is there any reason (Dan, Russ) I
Identified patient information specifically? Or de-identified also? If
de-identified, this implies that all I2B2 instances (and any other
services that use the data warehouses) use SSL. Which is not a bad idea,
but we need to be sure everyone understands this.
On 10/27/2014 05:36 PM, Dan
On 10/21/2014 09:52 AM, Verhagen, Laurel A wrote:
After writing the agenda, I received the following from Steve Fennel:
1)How will GPC data in motion be protected? /All data in motion will
be encrypted. Specially, data files will be sent via SCP.
Alternatively, if the application involves
On 10/17/2014 10:57 AM, GPC Informatics wrote:
#141: differentiate well-child visits, sick visits, and chronic visits
(utilization)
+
Reporter: dconnolly | Owner: bokov
Type: design-issue| Status: assigned
Yes, I'm fully in agreement there-- no direct, unlimited queries by
investigators. Or under normal circumstances, us, for that matter. The
only variable parts are the patient/visit sets.
I see the goal of the initial cohort work is learning how to generalize
these queries so they can be
Kind thanks to KUMC and the sites that volunteered to test.
With help from Wisconsin and MCW so far, I have a lot of revisions to
add to the original script that make the output smaller, the syntax less
Oracle-specific, and eliminate or scrub certain fields. If you're not
one of the test sites,
*From:* gpc-dev-boun...@listserv.kumc.edu
[gpc-dev-boun...@listserv.kumc.edu] on behalf of Alex Bokov
[bo...@uthscsa.edu]
*Sent:* Monday, October 06, 2014 12:57 PM
*To:* gpc-dev@listserv.kumc.edu
*Subject:* Example (Re: Empirical Data Dictionary)
Kind thanks to KUMC and the sites that volunteered
Thank you very much. I'm happy to help at our end by making the query
less Oracle-specific if you let me know which statements generate errors.
Have a great weekend.
On 10/03/2014 02:25 PM, Verhagen, Laurel A wrote:
Hi Alex,
Just wanted to let you know that Marshfield is working on this as
The linked definition doesn't preclude redundant entries resulting from
multiple encounters taking place on the same day (and these are not
rare, at least at the two GPC sites I've worked with so far). This is
deeper than terminology. The pragmatic question is: what should be in
each row of
This is a very important question-- I can't imagine doing a meaningful
retrospective study without addressing it.
I noticed that whenever an encounter has a diagnosis with MODIFIER_CD =
'DiagObs:PROBLEM_LIST' that encounter will also contain the same
diagnosis but with MODIFIER_CD =
And, given how much of a difference mods make for diagnoses, should we
be expecting analogous gotchas for modifiers on medications?
Does anybody know what PRN means?
Does anybody know under what circumstances Cumulative Daily Dose is
used and under what circumstances Medication Administration
As I was trying to count and pivot data from I2B2 today, I noticed that
our CONCEPT_DIMENSION table (in the BLUEHERONDATA schema if you use the
HERON ETL code, in the I2B2DEMODATA schema by default presumably) has
duplicate CONCEPT_CD's.
Here is the resulting question to the I2B2 Install Help
Here is a link to San Antonio's current revision of the CDM Compliance
Worksheet
https://pcornet.centraldesktop.com/p/eAAAEcplAEUPhn0
There will be a few more updates to the Vitals table next week, but here
is what we have for now.
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