Hi,
I am curious if anyone is applying indexes to the SAS CDM tables.
For example, putting on a unique index on the PATID in the DEMOGRAPHIC table.
One way it can be done is with "proc sql" steps using "create index" commands.
I am guessing that this could dramatically impact the time needed
it is more specific
than "Re: Contents of Gpc-dev digest..."
Today's Topics:
1. UNMC - June 2019 Hashed SSDI file, can not open zip file with
specified encryption key (Pedersen, Jay G)
--
Messag
Hi,
This is regarding the distributed hashed SSN Death Index file from June 2019
form KUMC.
I have downloaded the files, but am failing to unzip the created zip file which
holds the CSV file with the hashed SSN Death Index.
I have actually gone through the procedure twice,
downloading
Hi,
I attach a python script which works with MS SQL Server and creates a table
UNMC_PATID_TO_HASHED_SSN_DOB, which has PATIENT_IDE and SSN_DOB_HMAC fields.
The SSN_DOB_HMAC is computed using the hash key provided by KUMC when the
hashed SSN Death Index is transferred and using the python
.
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE 68198-5900
402-559-9487 (office)
402-739-3496 (mobile)
From: McNeeley, Todd Alexander
Sent: Tuesday, May 14, 2019 9:03 AM
To: Pedersen, Ja
)
From: Pedersen, Jay G
Sent: Monday, May 13, 2019 7:09 PM
To: gpc-dev@listserv.kumc.edu
Cc: Pedersen, Jay G
Subject: UNMC, SQL-server based i2b2, special configuration for parallel
queries?
Hi,
We are starting to run queries against our MS-SQL based i2b2 in Nebraska.
We are seeing
Hi,
We are starting to run queries against our MS-SQL based i2b2 in Nebraska.
We are seeing what seems to be blocking of queries that are trying to be
executed in parallel by different users.
Does the access to the Fact table by 'active query #1' cause 'active query #2'
which also needs to
Hi,
At UNMC, we are deep into the porting from Oracle to MS-SQL for our i2b2
instance.
We are using MS-SQL 2014.
We are interested in knowing how other sites are indexing their fact table.
The indexing 'by default' for the fact table when installing i2b2 appears to be:
I am curious if that is
er
985900 Nebraska Medical Center
Omaha NE 68198-5900
402-559-9487 (office)
402-739-3496 (mobile)
From: Dan Connolly
Sent: Friday, March 1, 2019 9:26 AM
To: Pedersen, Jay G
Cc: gpc-dev@listserv.kumc.edu
Subject: Re: MS-SQL hashing function?, re: Death index fi
Hi,
I am wondering if anyone knows if it is possible
to create a MS-SQL analog of the following
Oracle function ... which provides hasing
of SSN and DOB:
I am hoping Dan Connolly might be able to provide direction.
The fallback is to create a python script to
interface to MS-SQL and create
Medical Center
Omaha NE 68198-5900
402-559-9487 (office)
402-739-3496 (mobile)
From: GPC Informatics
Sent: Thursday, February 14, 2019 1:55 PM
To: dconno...@kumc.edu; Narayana, Yeshwanth R; Campbell, James R
Cc: dbud...@kumc.edu; rwait...@kumc.edu; Pedersen,
Hi,
At UNMC, we are porting from our Oracle database to MS-SQL Server.
I am curious how other sites using MS SQL-Server are indexing
the OBSERVATION_FACT table.
Can anyone send me the DDL used to create and index the
OBSERVATION_FACT table that you are using?
Any comments on performance of
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE 68198-5900
402-559-9487 (office)
402-739-3496 (mobile)
From: Dan Connolly
Sent: Friday, January 25, 2019 8:37:29 AM
To: Pedersen, Jay G; gpc-dev@listserv.kumc.edu
Subject: RE: i2b2 instal
Docker-based instructions/hints are welcome!
Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE 68198-5900
402-559-9487 (office)
402-739-3496 (mobile)
From: Pedersen, Jay G
Sent
Hi,
UNMC is switching from its Oracle-based i2b2 installation
to one that is MS-SQL based, and using a Wildfly web server
to support the i2b2 web (Java) software.
We would like to install i2b2 client version 1.7.10 (or possibly 1.7.09c)
and of course have a MS-SQL database that supports
Hi,
UNMC can pick up the scribing for the GPC meeting tomorrow.
Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
From: Gpc-dev on behalf of
gpc-dev-requ...@listserv.kumc.edu
Sent: Monday, August 6, 2018 3:12:59 PM
96 (mobile)
____
From: Pedersen, Jay G
Sent: Tuesday, May 15, 2018 3:08:42 PM
To: gpc-dev@listserv.kumc.edu
Subject: UNMC -- trying to use R Data Builder -- having an issue "error from
back-end, mismatched tag"
Hi,
We are attempting to use the historic R Data builder plugin,
install
Hi,
We are attempting to use the historic R Data builder plugin,
installed about 4 years ago. It has worked for us in the past
but is now doing something we don't understand.
In the past, this resulted in a JSON file being created on our de-identified
server in
James R; Pedersen, Jay G
Subject: Re: [gpc-informatics] #676: Postgres SNOW SHRINE nodes (UNMC , MCW)
time out
Non-UNMC email
#676: Postgres SNOW SHRINE nodes (UNMC , MCW) time out
--+
Reporter: ynarayana | Owner: mish
; m...@wisc.edu; dconno...@kumc.edu
Cc: Campbell, James R; McClay, James C; Pedersen, Jay G
Subject: Re: [gpc-informatics] #676: SNOW SHRINE- UNMC production
Non-UNMC email
#676: SNOW SHRINE- UNMC production
--+
Reporter: ynarayana |
Hi,
The following URL points to the web page at UNMC with the
FULL release metadata for shrine with additions for Medications.
It will be updated this week with Lab additions (LOINC).
The medications update includes historically comprehensive
RxNorm coding through March 2018.
ty of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE 68198-5900
402-559-9487 (office)
402-739-3496 (mobile)
From: Dan Connolly <dconno...@kumc.edu>
Sent: Wednesday, March 21, 2018 9:23:01 AM
To: Pedersen, Jay G; gpc-dev@listserv.kumc.edu
Subject: R
Hi,
My understanding is that some of the GPC sites in the SNOW SHRINE
network, have NAACCR metadata installed in addition to
Harvard's metadata. For those sites, they see a SCILHS folder
and a separate NAACCR folder in the SHRINE client.
Is that correct?
If UNMC wanted to support the
Hi,
SUMMARY
I am trying to fix issues with the UNMC SHRINE Spoke ... and believe
that I have problems with the AdapterMappings.csv file.
I am hoping someone with a working SHRINE Spoke implementation could
share with me (or point me to) a working AdapterMappings.csv or .xml file
that
Hi,
We are obtaining HCPCS codes from CPT_CODE field from the ARPB_TRANSACTIONS
table,
when the first character of CPT_CODE is not numeric.
We have found 865 distinct HCPCS codes, including 179 distinct 'J' codes.
However, this did not include the J9355 code.
Jay Pedersen, M.A.
Department
Hi,
Can anyone who is using Postgres as the database for their
SHRINE spoke, tell me the exact indexes that they are using
for the observation_fact table?
We saw the following for the "demo data" postgres database,
but I am not sure all of the indexes are needed. For example,
there was an
edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Gpc-dev digest..."
Today's Topics:
1. Re: Gpc-dev Digest, Vol 39, Issue 48 (Pedersen, Jay G)
--
Message: 1
Date: W
uot;
Today's Topics:
1. Re: Gpc-dev Digest, Vol 39, Issue 47 (Pedersen, Jay G)
--
Message: 1
Date: Wed, 24 May 2017 23:14:13 +
From: "Pedersen, Jay G" <jay.peder...@unmc.edu>
To: "gpc-dev@listserv.k
Hi,
Regarding loading the ACS and GEOCODING information into Oracle:
We created two tables and imported CSV files with the ACS and GEOCODING table
information,
and imported CSV files that we created from the hackathon notes and from the
GEOCODING files that we received (again -- thanks to
/Microbiology
University of Nebraska Medical Center
985900 Nebraska Medical Center
Omaha NE 68198-5900
402-559-9487 (office)
402-739-3496 (mobile)
From: Campbell, James R
Sent: Saturday, May 13, 2017 11:34:34 AM
To: Klann, Jeffrey G.; Pedersen, Jay G; gpc-dev@listserv.kumc.edu
Hi,
I have access to the GPC redcap project "Socioeconomic Variables for Obesity
Survey"
However, I don't seem to be able to download a data dictionary related to the
project,
so that I can create an appropriate CSV file for uploading data to the project.
I need to know how to encode race,
2-559-9487 (office)
402-739-3496 (mobile)
From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu>
Sent: Monday, April 24, 2017 9:58:00 PM
To: Pedersen, Jay G; Dan Connolly
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Michael Prittie;
Campbell, James R
S
<dconno...@kumc.edu>
Sent: Monday, April 24, 2017 8:56:13 PM
To: Pedersen, Jay G
Cc: Hubert Hickman; Russ Waitman; gpc-dev@listserv.kumc.edu; Klann, Jeffrey G.;
Michael Prittie; Campbell, James R
Subject: Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient
Yes, it's on babel. B
)
From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu>
Sent: Monday, April 24, 2017 11:15:23 AM
To: gpc-dev@listserv.kumc.edu; Pedersen, Jay G; Campbell, James R;
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: Re: [gpc-informatics] #280: Medi
)
From: Klann, Jeffrey G. <jeff.kl...@mgh.harvard.edu>
Sent: Wednesday, April 12, 2017 3:35:31 PM
To: Campbell, James R; gpc-dev@listserv.kumc.edu; Pedersen, Jay G;
huhick...@nebraskamed.com; dconno...@kumc.edu; rwait...@kumc.edu
Cc: mprit...@kumc.edu
Subject: Re
l 10, 2017 9:44:52 AM
To: Campbell, James R; dconno...@kumc.edu
Cc: ngra...@kumc.edu; lpa...@kumc.edu; Pedersen, Jay G
Subject: Re: [gpc-informatics] #568: Response on BABEL is painfully slow
#568: Response on BABEL is painfully slow
---+-
R
I have found that watching the JBOSS log file is useful to help debug client
messages like "ERROR: ERROR" or "Database error".
In our case, the log file is on the CENTOS machine that the i2b2 Java code runs
on in the following location:
/var/log/jboss-as/server.log
tail -f
Hi,
Can anyone explain where the geocoding data that has been used in the GPC for
various projects is obtained from? If there is information in a ticket, that
would be all I would need.
Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
985900
Hi,
Looks like that fixed it. Thanks!
Jay Pedersen, M.A.
Department of Pathology/Microbiology
University of Nebraska Medical Center
From: Dan Connolly <dconno...@kumc.edu>
Sent: Thursday, December 29, 2016 8:46:54 PM
To: Pedersen, Jay G; g
Hi,
I am trying to update the UNMC NAACCR extract to match as closely as possible
to KUMC's NAACCR extract (hopefully exactly), following the procedure outlined
here:
https://informatics.gpcnetwork.org/trac/Project/wiki/NAACCR_ETL
I am attempting to extract the t_item, t_code and t_section
Hi,
I was able to use naaccr_prep.py to extract information for the
2 missing consented patients and upload that to the GPC RedCap tumor datamart.
This required determining the MRN was used in
the NAACCR files for these patients (there had been a MERGE event on the
MRN that was associated
/Microbiology
UNMC
From: Dan Connolly <dconno...@kumc.edu>
Sent: Monday, October 31, 2016 4:06:41 PM
To: Pedersen, Jay G; gpc-dev@listserv.kumc.edu
Subject: RE: BC Survey -- UNMC update, using the most recent NAACCR record when
multiple records exist for th
Hi,
I just updated the UNMC BC Survey #2 tumor datamart in GPC RedCap.
DETAILS
We are using the naaccr_prep.py method of creating redcap data directly from
the NAACCR input files.
We had issues where multiple NAACCR records (from multiple files) would exist
for the same tumor.
We
Hi,
This question is directed to Dan Connolly, but the result may be of interest to
the GPC in general.
I had a question about what we discussed last Friday. Recall that we used a
different field in our NAACCR data to identify a patient. I think it was
postion 50:57, and the value was NOT
: Dan Connolly [dconno...@kumc.edu]
Sent: Thursday, October 13, 2016 5:08 PM
To: Campbell, James R; Pedersen, Jay G; gpc-dev@listserv.kumc.edu
Subject: RE: UNMC -- BC survey -- issue with rxcui values for importing
per-medication into RedCap, rxcui values
OK, all relevant UNMC meds
Hi,
I think that perhaps I am running into the situation that Dan was describing on
the call yesterday.
I have 137 data rows in my per-tumor.csv file but RedCap says that it imported
123 rows.
When I examine my data, I am seeing :00 more than once for the same
study-id. This occurred 14
Hi,
Looking for insight into the following problem. When I try to import my
per-medication CSV files into RedCap, I get errors relating to the "rxcui"
values. Specifically:
378861
847229
847262
897121
1298947
I have these documented to mean (I think I have this right, can double-check as
formatics [d...@madmode.com]
Sent: Monday, September 19, 2016 10:14 AM
To: dconno...@kumc.edu; m...@wisc.edu; gkowal...@mcw.edu; jd...@umn.edu;
kwa...@uwhealth.org
Cc: bo...@uthscsa.edu; Pedersen, Jay G; badaga...@kumc.edu; ngra...@kumc.edu
Subject: Re: [gpc-informatics] #459: How to add GPC sites to
I will scribe tomorrow (Jay Pedersen, UNMC).
From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on
behalf of gpc-dev-requ...@listserv.kumc.edu [gpc-dev-requ...@listserv.kumc.edu]
Sent: Monday, August 29, 2016 10:46 AM
To:
...@madmode.com]
Sent: Tuesday, August 02, 2016 11:29 AM
To: e-chrischil...@uiowa.edu; dconno...@kumc.edu; rwait...@kumc.edu;
bradley-mcdow...@uiowa.edu; prakash-nadka...@uiowa.edu; jd...@umn.edu;
verhagen.lau...@mcrf.mfldclin.edu; mo...@health.missouri.edu;
bzscho...@kumc.edu; Pedersen, Jay G; gkowal
Hi,
I didn't perform the query at UNMC, but our (UNMC's) result appears to have the
following set of concept-codes in the exported observation_fact table (1 LOINC
code):
ICD9CM:279.06
ICD9CM:473.0
ICD9CM:473.9
ICD9CM:486
LOINC:2465-3
Jay Pedersen, M.A.
Department of Pathology/Microbiology
Hi,
I need a bit of direction.
Per the GPC meeting discussion on obtaining information on
procedures,conditions,diagnoses from the CDMV3 table for consented patients in
the breast cancer cohort ...
UNMC personnel have extracted this information into an Excel spreadsheet with 3
sheets for
Hi,
The following notes relate to the portion of the meeting that I attended (about
11:15-end). I had initially seen a notice that the meeting had been canceled
(at about 11:05), and I re-tried at 11:15 and found the meeting in progress.
Hi,
I am unsure if I can update this ticket.
However, relating to comment 47 in the ticket
"""UNMC - Incomplete submission as of 4/13; only one of three required files
included. Has this been corrected?"""
This was corrected. All 3 files were sent, I believe this occurred on
4/13/2016, but
Hi,
I was given a link within redcap.gpcnetwork.org to submit the Height+Weight
query. I believe the contact person is Alex Bokov in San Antonio on this
project.
The result "R Data Builder" file that we just created (an SQLITE file, ".db"
file), far exceeds the 200MB file size limit that I
Hi,
Can anyone indicate the method for sending the resulting R Data Builder file
for the Height and Weight survey? My understanding is that it goes to San
Antonio. I did not see detailed instructions on sending the result. The
result file is somewhat large -- a 4GB file (SQLITE ".db" file).
Hi,
I was unsure how to add this information to ticket #463, which I believe this
is associated with. But ...
I request that github user "praveenreddysudini", who is Praveen Sudini, a
developer at UNMC working on the PCORI project ... be allowed access to GITHUB
repository
Hi,
I realize that Tkt 377 was just closed. But just stating that UNMC is
interested in being able to obtain update(s) to the SSN Death index from the
GPC, if that is possible. We do use that information in our database refresh
process.
Jay Pedersen, M.A.
Department of
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