Re: [gpc-informatics] #513: ~3% missing breast-cancer diagnosis data due to opt-out at UMN

[Justin Dale]

The latter - general consent was revoked after they were properly consented
to the specific study.

As for the ability to include these patients, I'm still not sure the
appropriate (or best) way to do it.  We should be able to manually extract
their data from our warehouse and do our best to provide it in the desired
format but I don't think thats a sustainable model.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Mon, Jun 27, 2016 at 9:05 AM, McDowell, Bradley D <
bradley-mcdow...@uiowa.edu> wrote:

> So is it the case that these patients should never have been offered the
> opportunity to participate in the questionnaire or provide access to their
> medical records? Or (it seems more likely), did the patient revoke their
> implied general consent after being properly consented to our specific
> study?
>
> If the latter, it seems that the specific opt-in consent to participate in
> the breast cancer survey project (with option to provide med records) would
> override the general opt-out. With that in mind, I think we would
> definitely want to maintain the ability to include these patients in the
> survey dataset. Do we even have that ability, though?
>
> Brad
>
> -Original Message-
> From: Dan Connolly [mailto:dconno...@kumc.edu]
> Sent: Monday, June 27, 2016 8:36 AM
> To: Chrischilles, Elizabeth A; gpc-dev@listserv.kumc.edu; McDowell,
> Bradley D
> Subject: RE: [gpc-informatics] #513: ~3% missing breast-cancer diagnosis
> data due to opt-out at UMN
>
> The description says: "The missing 3 were excluded from our CDM build
> because they have since opted-out of having their data available for
> general research purposes."
>
> Is that clear enough?
>
> --
> Dan
>
> 
> From: Chrischilles, Elizabeth A [e-chrischil...@uiowa.edu]
> Sent: Saturday, June 25, 2016 9:33 AM
> To: gpc-dev@listserv.kumc.edu; Dan Connolly; McDowell, Bradley D
> Subject: RE: [gpc-informatics] #513: ~3% missing breast-cancer diagnosis
> data due to opt-out at UMN
>
> I'd like to understand the reasons for this.  Is it because these
> consented patients were unable to be linked for some reason or is there
> some governance reason or something else.  Thanks
>
> -Original Message-
> From: GPC Informatics [mailto:d...@madmode.com]
> Sent: Friday, June 24, 2016 5:49 PM
> To: dconno...@kumc.edu; McDowell, Bradley D
> Cc: Chrischilles, Elizabeth A
> Subject: Re: [gpc-informatics] #513: ~3% missing breast-cancer diagnosis
> data due to opt-out at UMN
>
> #513: ~3% missing breast-cancer diagnosis data due to opt-out at UMN
> --+
>  Reporter:  dconnolly |   Owner:  brad_mcdowell
>  Type:  problem   |  Status:  assigned
>  Priority:  major |   Milestone:  bc-dx-px
> Component:  data-sharing  |  Resolution:
>  Keywords:|  Blocked By:
>  Blocking:  448   |
> --+
> Changes (by dconnolly):
>
>  * owner:  jdale => brad_mcdowell
>  * status:  new => assigned
>
>
> Comment:
>
>  Brad, what would be the impact if UMN didn't manage to share diagnoses
> and  procedures for 3 of their 98 consented patients?
>
> --
> Ticket URL: <
> http://informatics.gpcnetwork.org/trac/Project/ticket/513#comment:1>
> gpc-informatics <http://informatics.gpcnetwork.org/>
> Greater Plains Network - Informatics
> ___
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Re: [gpc-informatics] #513: ~3% missing breast-cancer diagnosis data due to opt-out at UMN

[Justin Dale]

Thanks Dan.

Our i2b2 and CDM are only loaded with patients who have NOT explicitly
opted-out of having their data available for general research purposes as
part of the consent process within the healthcare system. When we ran the
initial breast-cancer cohort query, all of the patients that met the
criteria had not opted-out.  Since then, 3 of those patients have
opted-out, or indicated they do not want their data to be available for
general research purposes.  So this means we no longer include them in i2b2
or our CDM builds/loads.  However, since they have consented specifically
for the breast cancer study and as I understand the rules, their data can
still be used for that study.  Since these patients still exist within our
data warehouse, we need to figure out how to make their data available
through some type of consent flag within i2b2/CDM (which may be problematic
if our changes do not conform to the standard) or some other type of
generally accepted approach.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Mon, Jun 27, 2016 at 8:35 AM, Dan Connolly <dconno...@kumc.edu> wrote:

> The description says: "The missing 3 were excluded from our CDM build
> because they have since opted-out of having their data available for
> general research purposes."
>
> Is that clear enough?
>
> --
> Dan
>
> 
> From: Chrischilles, Elizabeth A [e-chrischil...@uiowa.edu]
> Sent: Saturday, June 25, 2016 9:33 AM
> To: gpc-dev@listserv.kumc.edu; Dan Connolly; McDowell, Bradley D
> Subject: RE: [gpc-informatics] #513: ~3% missing breast-cancer diagnosis
> data due to opt-out at UMN
>
> I'd like to understand the reasons for this.  Is it because these
> consented patients were unable to be linked for some reason or is there
> some governance reason or something else.  Thanks
>
> -Original Message-
> From: GPC Informatics [mailto:d...@madmode.com]
> Sent: Friday, June 24, 2016 5:49 PM
> To: dconno...@kumc.edu; McDowell, Bradley D
> Cc: Chrischilles, Elizabeth A
> Subject: Re: [gpc-informatics] #513: ~3% missing breast-cancer diagnosis
> data due to opt-out at UMN
>
> #513: ~3% missing breast-cancer diagnosis data due to opt-out at UMN
> --+
>  Reporter:  dconnolly |   Owner:  brad_mcdowell
>  Type:  problem   |  Status:  assigned
>  Priority:  major |   Milestone:  bc-dx-px
> Component:  data-sharing  |  Resolution:
>  Keywords:|  Blocked By:
>  Blocking:  448   |
> --+
> Changes (by dconnolly):
>
>  * owner:  jdale => brad_mcdowell
>  * status:  new => assigned
>
>
> Comment:
>
>  Brad, what would be the impact if UMN didn't manage to share diagnoses
> and  procedures for 3 of their 98 consented patients?
>
> --
> Ticket URL: <
> http://informatics.gpcnetwork.org/trac/Project/ticket/513#comment:1>
> gpc-informatics <http://informatics.gpcnetwork.org/>
> Greater Plains Network - Informatics
> ___
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Re: PCORnet data characterization calls

[Justin Dale]

Thanks Keith.  Upon reviewing our Empirical Data Characterization report we
did have questions about how to approach fixing.  Unfortunately we were
unable to call-in at those times.

We're trying to figure out the appropriate process for working through CDM
data issues.  For example, we have an issue where 6% of our patients have
an enrollment end date in the future, which is beyond what PCORI expects.
Our enrollment data is encounter-based so these end dates are being sourced
from encounters that have already been scheduled in the future.  We feel
this is appropriate but will need further clarification.  Similarly, on the
Tuesday dev call we discussed how we should handle encounter types like
phone calls, cancelled appts, lab results, etc, should we be excluding
encounters that don't have a dx or procedure associated with them, and if
we need to make changes to fix these issues, are the changes executed when
loading i2b2 or modifying the SCHILS code.

In the "Update on PCORnet DataMart Readiness Evaluation" document Russ
shared it states:

1. By Friday May 20th, DataMarts will send the DRN OC a written response
that describes how they propose to address the issues identified and the
time required to implement the solution. Appendix B contains a template for
this response. If the issue cannot be fixed, the DataMart should explain
why.

Does that mean each site should individually be working with the
coordinating center to address CDM issues and applying the fixes locally?
Or should we first be working through these issues collectively as part of
the GPC?


Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Wed, May 4, 2016 at 4:46 PM, Wanta Keith M <kwa...@uwhealth.org> wrote:

> GPC dev team –
>
>
>
> If anyone is interested, Duke sent me these meeting times for PCORnet DCQ
> calls.  I’d suggest attending if you have questions about CDM, as a post
> mortem.  We all go through these queries, but in case you have questions,
> feel free to join.
>
>
>
> *Subtract an hour* for CDT on your calendars!  These are EDT.
>
>
>
> *May 5, 2016 at 2pm ET*
>
> 1-650-479-3207 Call-in toll number (US/Canada)
>
> Access code: 731 703 793
>
>
>
> *May 6, 2016 at 12pm ET*
>
> 1-650-479-3207 Call-in toll number (US/Canada)
>
> Access code: 736 965 276
>
>
>
>
>
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>
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Re: [gpc-informatics] #473: PCORnet CDMv3 SAS prep-to-research Readiness

[Justin Dale]

My mistake.  We just submitted the DCQ, which requires the annotated data
dictionary.

Justin

On Thu, Apr 28, 2016 at 12:26 PM, Verhagen, Laurel A <
verhagen.lau...@mcrf.mfldclin.edu> wrote:

> Justin,
>
> The Diagnostic Query (DQ) shouldn't require the Annotated Data
> Dictionary... just the Data Characterization Query. Did James indicate
> otherwise?
>
> Thanks,
> Laurel
>
> -Original Message-
> From: GPC Informatics [mailto:d...@madmode.com]
> Sent: Thursday, April 28, 2016 12:22 PM
> To: bzscho...@kumc.edu; Verhagen, Laurel A; jd...@umn.edu;
> dconno...@kumc.edu; b...@uthscsa.edu; ngra...@kumc.edu; mprit...@kumc.edu;
> nate.apa...@cerner.com; mo...@health.missouri.edu; campb...@unmc.edu;
> kwa...@uwhealth.org; ashok.mudgapa...@unmc.edu; jmcc...@unmc.edu;
> m...@wisc.edu; jay.peder...@unmc.edu
> Cc: gpc-dev@listserv.kumc.edu; darcy.lou...@duke.edu
> Subject: Re: [gpc-informatics] #473: PCORnet CDMv3 SAS prep-to-research
> Readiness
>
> #473: PCORnet CDMv3 SAS prep-to-research Readiness
> -+
>  Reporter:  bzschoche|   Owner:  lv
>  Type:  enhancement  |  Status:  assigned
>  Priority:  major|   Milestone:  data-domains3
> Component:  data-stds|  Resolution:
>  Keywords:   |  Blocked By:  381, 486
>  Blocking:   |
> -+
>
> Comment (by jdale):
>
>  UMN submitted the DQ results today (4/28/16) minus the ETL annotated
> data  dictionary. In all the chaos of trying to get the query to run we
> overlooked it.  We verified with James Topping from Duke it was ok to
> submit the results right now and the ETL document when complete.
>
>  Our previous issues were definitely related to writing the SAS temp
> files  to network storage vs local.  We increased the size of the local
> disk to  accommodate the large SAS temp files and that made all the
> difference.
>
> --
> Ticket URL: <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_trac_Project_ticket_473-23comment-3A55=BQICaQ=KNVzINr6WAqWApikNSnyDeOu0ck0iFwcrMz92MxUhIs=A2PXk2ZGVGBzoEOQMwrrbqse0CnDMUgS4P3-3HOTSAwE8Vfvoc1Wm0NCYFbuU-_5=0kO7xHBpQhRLAiWz9dsSQ3ypUjJXaihjed7X3XahWYA=Oze0gEDZPiTyLhGMxLzL9Si0_Z0HdI95qyeaZzWovN0=
> > gpc-informatics <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_=BQICaQ=KNVzINr6WAqWApikNSnyDeOu0ck0iFwcrMz92MxUhIs=A2PXk2ZGVGBzoEOQMwrrbqse0CnDMUgS4P3-3HOTSAwE8Vfvoc1Wm0NCYFbuU-_5=0kO7xHBpQhRLAiWz9dsSQ3ypUjJXaihjed7X3XahWYA=9Lon3fWbAi1nkYOw0iBP98r6jvRhcli72ak9KmLKp2Q=
> > Greater Plains Network - Informatics
>
> __
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Re: [gpc-informatics] #473: PCORnet CDMv3 SAS prep-to-research Readiness

[Justin Dale]

Could someone point me to the URL for uploading the DQ result file?  I
thought it was on https://pcornet.imeetcentral.com/ but its not clear to me
where. Or do we email directly to Darcy?  Thanks.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Mon, Mar 28, 2016 at 10:07 AM, GPC Informatics <d...@madmode.com> wrote:

> #473: PCORnet CDMv3 SAS prep-to-research Readiness
> -+
>  Reporter:  bzschoche|   Owner:  lv
>  Type:  enhancement  |  Status:  assigned
>  Priority:  major|   Milestone:  data-domains3
> Component:  data-stds|  Resolution:
>  Keywords:   |  Blocked By:  381, 486
>  Blocking:   |
> -+
>
> Comment (by jdale):
>
>  Minnesota ran into a problem during processing the DQ file on Friday
>  afternoon and we were unable to resolve the issue in time.  I emailed
>  Darcy saying we'll have the DQ results completed by Wednesday, 3/30/16 at
>  5pm.
>
> --
> Ticket URL: <
> http://informatics.gpcnetwork.org/trac/Project/ticket/473#comment:34>
> gpc-informatics <http://informatics.gpcnetwork.org/>
> Greater Plains Network - Informatics
>
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Re: UMN Q3 quality results in the GPC REDCap database.

[Justin Dale]

Thanks for your help Tom and for the explanation.  I think the issue was
that I was selecting the "column" option for the record format when
importing because I interpreted the "row" option to be a file that contains
many rows vs a "column" file that would have many columns and just one row.
Anyway, now I know for future imports and happy that you're able to have
that extra cup of pumpkin spice coffee!

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Fri, Oct 23, 2015 at 8:11 AM, Thomas Mish <m...@wisc.edu> wrote:

> Justin,
>
>
> I went to do an import on the dataset you sent me and ran into no errors.
> The way you have your data import set the record format is “Rows” (most of
> the QA datasets use “Columns” – but no big deal); the dates are all the
> default format, those are really the only import options. I have no clue
> why this worked for me and not for you. I’m a little surprised, I thought
> I’d at least have a bit of a tussle on my hands this morning. I guess that
> leaves me with a few extra minutes for an extra cup of coffee this morning.
>
>
>
> Cheers and congrats on being the first group to import your results into
> the REDCap database.
>
>
>
>
>
> -TM
>
>
>
>
>
>
>
> *From:* dalex...@umn.edu [mailto:dalex...@umn.edu] *On Behalf Of *Justin
> Dale
> *Sent:* Thursday, October 22, 2015 8:30 AM
> *To:* Thomas Mish
> *Subject:* Re:
>
>
>
> Thanks.  UMN Q3 file attached. Let me know if you see anything that would
> be causing the errors.
>
>
> Regards,
>
>
>
> Justin Dale
>
> Manager - Research Development and Support
>
> University of Minnesota
>
> Academic Health Center - Office of Information Systems
>
> Phone: 612.624.9747
>
> Fax: 612.624.7458
>
> jd...@umn.edu
>
>
>
> On Thu, Oct 22, 2015 at 8:25 AM, Thomas Mish <m...@wisc.edu> wrote:
>
>
>
> Previous results as reported by REDCAp
>
> *___*
>
> *Thomas F. Mish Jr.*  -   Informatics Systems Specialist
>
> SMPH-ITBiomedical Informatics Services
>
> School of Medicine and Public Health, UW-Madison
>
> m...@wisc.edu  -  (608)616-0362
>
>
>
>
>
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Re: [gpc-informatics] #350: geocoding: distribute census, ACS data to sites

[Justin Dale]

I'm still waiting for contacts from WISC and CMH.  I believe I've shared
the files with contacts from all other sites.


Justin

On Mon, Oct 12, 2015 at 9:58 AM, GPC Informatics  wrote:

> #350: geocoding: distribute census, ACS data to sites
> ---+
>  Reporter:  dconnolly  |   Owner:  jdale
>  Type:  task   |  Status:  assigned
>  Priority:  major  |   Milestone:  geocode-1
> Component:  data-stds  |  Resolution:
>  Keywords: |  Blocked By:
>  Blocking:  140|
> ---+
>
> Comment (by dconnolly):
>
>  Justin, what's left to do on this?
>
>  If nothing (i.e. if all relevant sites have confirmed receipt) then please
>  close this.
>
> --
> Ticket URL: <
> http://informatics.gpcnetwork.org/trac/Project/ticket/350#comment:8>
> gpc-informatics 
> Greater Plains Network - Informatics
>
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Re: gpc-dev 6 Oct agenda and meeting notes

[Justin Dale]

I need to send my regrets for tomorrow's call as I will be out of the
office.

I've asked David for the location of the geocoding files.  Once I have that
info I will place the files in the same sFTP directory that the original
data was delivered and will let Mei Liu from KUMC know.

I would have put this in the comments info on the trac ticket
<https://informatics.gpcnetwork.org/trac/Project/ticket/350> but I just
reset my password and now I can'l login.  I believed this happened last
time I tried to reset my password.  Nathan Graham, can you assist with this
again?  This is for my jdale username.  Thanks.



Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Mon, Oct 5, 2015 at 5:11 PM, Dan Connolly <dconno...@kumc.edu> wrote:

> What else for tomorrow?
>
> shared notes for Oct 6
> <https://docs.google.com/document/d/1DQC_AV8U0A31JS_louPiU_UD2k_UY4bkkNWPrAaT7yU/edit>;
> current snapshot:
>
> --
>
>
>1.
>
>Convene, take roll, review records and plan next meeting
>1.
>
>   ​Meeting ID and access code: 817-393-381
>   <https://global.gotomeeting.com/meeting/join/817393381>; call +1
>   (571) 317-3131
>   2.
>
>   roll: all 12 DevTeams
>   <https://informatics.gpcnetwork.org/trac/Project/wiki/DevTeams>
>   represented? KUMC, CMH, UIOWA, WISC, MCW, MCRF, UMN, UNMC, UTHSCSA, 
> UTSW,
>   MU, IU
>   Reminder - put institution after your name in GoToMeeting
>   preferences
>   1.
>
>  today's scribe: KUMC
>  3.
>
>   comments on the agenda? on last week’s notes (#12
>   <https://informatics.gpcnetwork.org/trac/Project/ticket/12>)? recent
>   tickets
>   opened/closed
>   <https://informatics.gpcnetwork.org/trac/Project/timeline> FYI
>   (note also recent ticket comments report
>   <https://informatics.gpcnetwork.org/trac/Project/report/13>):
>   1.
>
>  #367 (update KUMC babel terms w.r.t ICD10) closed
>  
> <https://informatics.gpcnetwork.org/trac/Project/ticket/367#comment:2>
>  1.
>
> #375 (KUMC Babel terms lack "KUMC" prefix on tooltips
> 
> <https://informatics.gpcnetwork.org/trac/Project/ticket/375#comment:1>
> 2.
>
>  #376 (data builder limited to `like
>  concept_dimension.concept_path` metadata) created
>  <https://informatics.gpcnetwork.org/trac/Project/ticket/376>
>  3.
>
>  #370 (compresed file upload for use in babel DB IDE) reopened
>  
> <https://informatics.gpcnetwork.org/trac/Project/ticket/370#comment:2>
>  4.
>
>  #378 (Estimate maximum cohort size from KUMC for CMS/Duke
>  collaboration) closed
>  
> <https://informatics.gpcnetwork.org/trac/Project/ticket/378#comment:1>
>  5.
>
>  #178 (determine whether last.visit is the last fulfilled visit
>  or the last ...) closed
>  
> <https://informatics.gpcnetwork.org/trac/Project/ticket/178#comment:16>
>  4.
>
>   Next Meeting: 13 October Scribe Volunteer?
>   2.
>
>#377 (Distribute Social Security Death Master file to sites) created
><https://informatics.gpcnetwork.org/trac/Project/ticket/377>
>3.
>
>milestone:geocode-1
>    <https://informatics.gpcnetwork.org/trac/Project/milestone/geocode-1>
>1.
>
>   #350 <https://informatics.gpcnetwork.org/trac/Project/ticket/350> 
> geocoding:
>   distribute census, ACS data to sites
>   <https://informatics.gpcnetwork.org/trac/Project/ticket/350>
>   1.
>
>  Van Riper Oct 2: “I will work with Justin Dale at the UMN CTSI
>  to get you access to your data via SFTP”
>  4.
>
>milestone:data-domains3
><https://informatics.gpcnetwork.org/trac/Project/milestone/data-domains3>,
>drn-query-1
><https://informatics.gpcnetwork.org/trac/Project/milestone/drn-query-1>
>1.
>
>   #160 <https://informatics.gpcnetwork.org/trac/Project/ticket/160> 
> reproducible
>   GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4)
>   <https://informatics.gpcnetwork.org/trac/Project/ticket/160>
>   2.
>
>   DRN status at GPC sites
>   
> <https://docs.google.com/spreadsheets/d/1Lg5fAHV5_rBT_FyF4_8NDuZC7KlNapLai90LEkdnxpI/edit#gid=0>
>   5.
>
>milestone:cohor

Re: [gpc-informatics] #329: UMN cancer tumor registry i2b2 path punctuation varies from HERON design

[Justin Dale]

I believe the version of our cancer cases ontology on babel is outdated.
However, I'm not sure our most recent version conforms to the standard
paths you listed.  You will need to forgive me as one of the people who
helped with this is no longer on the team so I'm trying to put the pieces
back together.  I've attached a spreadsheet with the record output from our
i2b2 ontology table for the example you provided.  Would you mind creating
a new line that represents what the correct values should be for each
column?  This would be a tremendous help in our efforts to correct it.
Thanks.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Wed, Aug 12, 2015 at 11:44 AM, GPC Informatics d...@madmode.com wrote:

 #329: UMN cancer tumor registry i2b2 path punctuation varies from HERON
 design
 ---+---
  Reporter:  dconnolly  |   Owner:  jdale
  Type:  problem|  Status:  new
  Priority:  major  |   Milestone:  cohort-char-
 Component:  data-stds  |  bc-db
  Keywords:  breast-cancer-cohort data-quality  |  Resolution:
  Blocking: |  Blocked By:
 ---+---
 Changes (by dconnolly):

  * priority:  minor = major
  * milestone:  babel-lec2-prep = cohort-char-bc-db


 Comment:

  This is critical path for the upcoming breast cancer data federation.

 --
 Ticket URL: 
 http://informatics.gpcnetwork.org/trac/Project/ticket/329#comment:1
 gpc-informatics http://informatics.gpcnetwork.org/
 Greater Plains Network - Informatics



UMN Cancer Ontology - 0400 Skin.xlsx
Description: MS-Excel 2007 spreadsheet
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Re: flowsheets in i2b2

[Justin Dale]

Thanks Dan - this is very helpful.  We're going to start with a subset
(200K encounters w/ related flowsheets) to test the process and
performance.  More questions may follow as we make our way down the rabbit
hole.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Wed, Aug 5, 2015 at 11:10 AM, Dan Connolly dconno...@kumc.edu wrote:

 1. yes, multiselect was a pain. the relevant HERON code is
 epic_flowsheets_multiselect.sql
 https://informatics.kumc.edu/work/browser/heron_load/epic_flowsheets_multiselect.sql

 We mentioned this in our AMIA 2011 paper
 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243191/:

 Measures documented as structured choices allowing multiple responses
 (e.g. “Dressing Status” is “clean dry and intact” and “reinforced”) are
 stored as a concatenated string that must be separated into individual
 observations within i2b2.

 2. We started with discrete data only as well.

 We're now working on adding de-identified flowsheet notes to HERON
 utilizing Medical College of Wisconsin's ​Unstructured Notes
 Deidentification
 https://bitbucket.org/MCW_BMI/unstructured-notes-deidentification/overview
 methodology. Wish us luck...

 3. Flowsheet observations dominate our i2b2 observation_fact table. 889M
 in the McMillan Marsh release
 https://informatics.kumc.edu/work/blog/heron-mcmillan-marsh-update. Our
 typical ETL timing breakdown
 https://informatics.kumc.edu/work/wiki/HeronLoad#heron_load shows
 epic_flowsheets takes 15+ hours (out of something like 40 or 60).

 Our latest release has 939M flowsheet facts; the main flowsheet ETL task
 took quite a bit more than 15 hrs:

 2015-07-18 00:52:16   for 1 day, 11:34:00.379441  1 
 load_epic_flowsheets

 Query time performance is pretty good with ~1.5B facts, though we do use
 solid state storage and bitmapped indexes (i2b2_facts_index.sql
 https://informatics.kumc.edu/work/browser/heron_load/i2b2_facts_index.sql).
 My off-hand estimate is: 6 to 60seconds is typical, with more complex
 queries taking longer.

 We have a real-time how busy is heron? page that shows the run-time of
 recent queries as well as a performance regression suite that we run at
 release time and weekly. I could get details from those if it's important.

 --
 Dan

 --
 *From:* dalex...@umn.edu [dalex...@umn.edu] on behalf of Justin Dale [
 jd...@umn.edu]
 *Sent:* Tuesday, August 04, 2015 10:10 PM
 *To:* Dan Connolly
 *Cc:* Tim Meyer
 *Subject:* flowsheets in i2b2

 Dan,

 Wondering if you had any words of wisdom to share for loading flowsheet
 data in i2b2?  We've drawn up plans for our environment but wanted to check
 with you to see if there were any gotcha moments or valuable
 lessons-learned.  Couple of the items we need to address:
 1. custom list values for measure values: stored as semi-colon separated
 list in the Clarity table when multiple values have been selected.  we'll
 need to parse each of these values and load as individual facts
 2. we're going to exclude any non-numeric and non custom list measure
 values because being able to run a query to just check if the fact exists
 or not does not seem valuable.
 3. not sure what to expect from i2b2 performance once we add nearly 3
 billion more rows to the database.  considering starting with a subset of
 500K to both test our i2b2 loader and performance.

 Appreciate any information you can provide.  Thanks Dan.


 Regards,

 Justin Dale
 Manager - Research Development and Support
 University of Minnesota
 Academic Health Center - Office of Information Systems
 Phone: 612.624.9747
 Fax: 612.624.7458
 jd...@umn.edu

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Re: maternal, sibling linkage for antibiotic obesity study?

[Justin Dale]

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.edu wrote:

  Do you know how we get these from CLARITY?

 --
 Dan

  --
 *From:* Campbell, James R [campb...@unmc.edu]
 *Sent:* Thursday, May 07, 2015 11:59 AM
 *To:* Dan Connolly; gpc-dev@listserv.kumc.edu; GPC Obesity Research Team (
 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.edu

 Office 402-559-7505

 Secretary 402-559-7299

 Fax 402-559-8396

 Pager 402-888-1230



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



 Question 4 of the antibiotic survey (#277
 https://informatics.gpcnetwork.org/trac/Project/ticket/277) asks about
 maternal and sibling links. We have an issue in this area, #103
 https://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

 The information in this e-mail may be privileged and confidential,
 intended only for the use of the addressee(s) above. Any unauthorized use
 or disclosure of this information is prohibited. If you have received this
 e-mail by mistake, please delete it and immediately contact the sender.

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Re: GPC-Dev Agenda 4-21

[Justin Dale]

Minnesota - Version 6.0.18

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Tue, Apr 21, 2015 at 10:42 AM, Thomas F Mish m...@wisc.edu wrote:

  Wisconsin is at 5.9.mumble...

 I don't currently have an ETA for getting to 6.1.x.  We tend to stick with
 LTS releases by policy. Without digging up my REDCap wiki username and
 password, does anyone know what version that would be?

 -TM


 On 4/21/2015 9:09 AM, Munns, Michael B wrote:

  UNMC 6.4.4



 Michael Munns

 Database Analyst

 402-559-3821



 *From:* gpc-dev-boun...@listserv.kumc.edu [
 mailto:gpc-dev-boun...@listserv.kumc.edu
 gpc-dev-boun...@listserv.kumc.edu] *On Behalf Of *Bos, Angela
 *Sent:* Monday, April 20, 2015 5:44 PM
 *To:* Dan Connolly; Apathy, Nate; gpc-dev@listserv.kumc.edu
 *Subject:* RE: GPC-Dev Agenda 4-21



 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
 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: 817-393-381
 https://global.gotomeeting.com/meeting/join/817393381; call +1 (571)
 317-3131

 b.roll: all 10 DevTeams
 https://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 (#12
 https://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

   i.recent tickets
 opened/closed FYI:

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

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

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

 d.Next Meeting April 28th: scribe?

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

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

 1.#158 Usable LOINC Labs - March 27 comment
 https://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:28
 proposes that  Jan 19 details
 https://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:20
 suffice

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

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

 1.milestone:data-quality3
 https://informatics.gpcnetwork.org/trac/Project/milestone/data-quality3

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

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

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

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

 1.Milestone: obesity-survey-def
 https://informatics.gpcnetwork.org/trac/Project/milestone/obesity-survey-def

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

 1.milestone:cohort-char1
 https://informatics.gpcnetwork.org/trac/Project/milestone/cohort-char1

 a.#258 https

Re: PopMedNet node at UNMC

[Justin Dale]

From Kyle at PCORnet:

I just wanted to clarify that there are no routing settings needed for
the File Distribution request type
https://popmednet.atlassian.net/wiki/display/DOC/File+Distribution. All
queries being distributed using this method will basically be a SQL program
with a workplan to walk you through the process of running it. The program
will have to be run manually against your data source, and therefore
requires no routings in the DataMart Client. This will be how all initial
phase I queries will be distributed.

So it's different than the first PopMedNet data mart client because now we
have to take the attached SQL file and run against our own CDM via SQL
Developer or whatever you preference.  Results of those queries then get
attached to the request when you submit it back through the datamart
client. Sounds like a future phase will integrate the CDM database back
into the datamart client.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Wed, Feb 11, 2015 at 10:17 AM, Mudgapalli, Ashok 
ashok.mudgapa...@unmc.edu wrote:

 You said the software is working just like we did first time. I have to
 ask couple of questions. Were you able to configure your local data source
 inside DM Client and ran the query from inside DM Client.
 This time it is different, I mean we have to pull the SQL file from DM
 client and execute separately. I appreciate your response. Thanks.

 Ashok

 -Original Message-
 From: gpc-dev-boun...@listserv.kumc.edu [mailto:
 gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Kowalski, George
 Sent: Tuesday, February 10, 2015 9:55 PM
 To: Justin Dale; Verhagen, Laurel A
 Cc: gpc-dev@listserv.kumc.edu
 Subject: Re: PopMedNet node at UNMC

 Laurel,

 I have the 5.0 DataMart  client connected to the:  https://api.pcornet.org
 Service URL and it seems to be working like the first time . Assuming we
 don’t have to hook it up to the “fake Postgres” data,  we’re ready to go
 here at MCW for the Basic Query.

 Thanks

 George

 From: Justin Dale jd...@umn.edumailto:jd...@umn.edu
 Date: Tuesday, February 10, 2015 at 7:24 PM
 To: LAUREL VERHAGEN verhagen.lau...@mcrf.mfldclin.edumailto:
 verhagen.lau...@mcrf.mfldclin.edu
 Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu 
 gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
 Subject: Re: PopMedNet node at UNMC

 Minnesota DataMart client is working as expected thanks to help from Kyle.

 Kyle said in his email:
 If you have the DataMart Client installed and it appears to be
 functioning correctly, please let me know and I will notify the DSSNI team
 that you have everything in place to respond to the Initial Basic Query
 against the CDM.

 Ashok and Laurel - did the DSSNI team send the request to you with the
 queries attached or did you download the queries and submit the query
 request to your datamart?



 Regards,

 Justin Dale
 Manager - Research Development and Support University of Minnesota
 Academic Health Center - Office of Information Systems
 Phone: 612.624.9747
 Fax: 612.624.7458
 jd...@umn.edumailto:jd...@umn.edu

 On Mon, Feb 9, 2015 at 10:20 AM, Verhagen, Laurel A 
 verhagen.lau...@mcrf.mfldclin.edumailto:verhagen.lau...@mcrf.mfldclin.edu
 wrote:
 Ashok,

 I have the same problem with the SQL server version that I’m trying to
 run. Sent an email to Jessica, but apparently the HPHCI offices are closed
 today due to weather.

 Thanks,
 Laurel

 From: Mudgapalli, Ashok [mailto:ashok.mudgapa...@unmc.edumailto:
 ashok.mudgapa...@unmc.edu]
 Sent: Monday, February 09, 2015 10:15 AM
 To: Verhagen, Laurel A; Justin Dale

 Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
 Subject: RE: PopMedNet node at UNMC

 If that is normal behavior, follow-up issue is …  I got the query file
 downloaded (zip file) and try to unzip, I am not able to unzip I tried many
 ways to unzip), the system says that the *.zip is invalid.  The file is
 oracle based query. Thanks.

 Ashok

 From: Verhagen, Laurel A [mailto:verhagen.lau...@mcrf.mfldclin.edu]
 Sent: Monday, February 09, 2015 9:52 AM
 To: Justin Dale; Mudgapalli, Ashok
 Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
 Subject: RE: PopMedNet node at UNMC

 Justin is correct. Instructions are to download the queries, run locally,
 then upload. This is different than the first connectivity test.

 Thanks,
 Laurel

 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: Monday, February 09, 2015 9:41 AM
 To: Mudgapalli, Ashok
 Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
 Subject: Re: PopMedNet node at UNMC

 We're seeing same screen when trying to edit the data model settings.
  I'm wondering if this is the intended behavior since these are all file
 distribution queries

Re: PopMedNet node at UNMC

[Justin Dale]

We (Minnesota) have uploaded our results - minus the enrollment numbers.

I did see in the instructions to include csv files for each table:
Instructions on how to respond to this request can be found here:
https://popmednet.atlassian.net/wiki/display/DOC/Executing+and+Responding+to+Requests.
  Please download the code, run it locally, and return the output tables in
CSV format as described in the Work plan.

The included workplan PDF was corrupt so we couldn't read it.  I did notify
Jessica of this issue.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Wed, Feb 11, 2015 at 11:04 AM, Mudgapalli, Ashok 
ashok.mudgapa...@unmc.edu wrote:

  Thanks for the clarification. Then we have finished our task
 successfully.



 Ashok



 *From:* dalex...@umn.edu [mailto:dalex...@umn.edu] *On Behalf Of *Justin
 Dale
 *Sent:* Wednesday, February 11, 2015 10:49 AM
 *To:* Mudgapalli, Ashok
 *Cc:* Kowalski, George; Verhagen, Laurel A; gpc-dev@listserv.kumc.edu

 *Subject:* Re: PopMedNet node at UNMC



 From Kyle at PCORnet:



 I just wanted to clarify that there are no routing settings needed
 for the File Distribution request type
 https://popmednet.atlassian.net/wiki/display/DOC/File+Distribution. All
 queries being distributed using this method will basically be a SQL program
 with a workplan to walk you through the process of running it. The program
 will have to be run manually against your data source, and therefore
 requires no routings in the DataMart Client. This will be how all initial
 phase I queries will be distributed.



 So it's different than the first PopMedNet data mart client because now we
 have to take the attached SQL file and run against our own CDM via SQL
 Developer or whatever you preference.  Results of those queries then get
 attached to the request when you submit it back through the datamart
 client. Sounds like a future phase will integrate the CDM database back
 into the datamart client.


Regards,



 Justin Dale

 Manager - Research Development and Support

 University of Minnesota

 Academic Health Center - Office of Information Systems

 Phone: 612.624.9747

 Fax: 612.624.7458

 jd...@umn.edu



 On Wed, Feb 11, 2015 at 10:17 AM, Mudgapalli, Ashok 
 ashok.mudgapa...@unmc.edu wrote:

 You said the software is working just like we did first time. I have to
 ask couple of questions. Were you able to configure your local data source
 inside DM Client and ran the query from inside DM Client.
 This time it is different, I mean we have to pull the SQL file from DM
 client and execute separately. I appreciate your response. Thanks.

 Ashok

 -Original Message-
 From: gpc-dev-boun...@listserv.kumc.edu [mailto:
 gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Kowalski, George
 Sent: Tuesday, February 10, 2015 9:55 PM
 To: Justin Dale; Verhagen, Laurel A

 Cc: gpc-dev@listserv.kumc.edu
 Subject: Re: PopMedNet node at UNMC

 Laurel,

 I have the 5.0 DataMart  client connected to the:  https://api.pcornet.org
 Service URL and it seems to be working like the first time . Assuming we
 don’t have to hook it up to the “fake Postgres” data,  we’re ready to go
 here at MCW for the Basic Query.

 Thanks

 George

 From: Justin Dale jd...@umn.edumailto:jd...@umn.edu
 Date: Tuesday, February 10, 2015 at 7:24 PM
 To: LAUREL VERHAGEN verhagen.lau...@mcrf.mfldclin.edumailto:
 verhagen.lau...@mcrf.mfldclin.edu
 Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu 
 gpc-dev@listserv.kumc.edumailto:gpc-dev@listserv.kumc.edu
 Subject: Re: PopMedNet node at UNMC

 Minnesota DataMart client is working as expected thanks to help from Kyle.

 Kyle said in his email:
 If you have the DataMart Client installed and it appears to be
 functioning correctly, please let me know and I will notify the DSSNI team
 that you have everything in place to respond to the Initial Basic Query
 against the CDM.

 Ashok and Laurel - did the DSSNI team send the request to you with the
 queries attached or did you download the queries and submit the query
 request to your datamart?



 Regards,

 Justin Dale
 Manager - Research Development and Support University of Minnesota
 Academic Health Center - Office of Information Systems
 Phone: 612.624.9747
 Fax: 612.624.7458
 jd...@umn.edumailto:jd...@umn.edu

 On Mon, Feb 9, 2015 at 10:20 AM, Verhagen, Laurel A 
 verhagen.lau...@mcrf.mfldclin.edumailto:verhagen.lau...@mcrf.mfldclin.edu
 wrote:
 Ashok,

 I have the same problem with the SQL server version that I’m trying to
 run. Sent an email to Jessica, but apparently the HPHCI offices are closed
 today due to weather.

 Thanks,
 Laurel

 From: Mudgapalli, Ashok [mailto:ashok.mudgapa...@unmc.edumailto:
 ashok.mudgapa...@unmc.edu]
 Sent: Monday, February 09, 2015 10:15 AM
 To: Verhagen, Laurel A; Justin Dale

 Cc: gpc-dev@listserv.kumc.edumailto:gpc-dev

Re: PopMedNet node at UNMC

[Justin Dale]

Minnesota DataMart client is working as expected thanks to help from Kyle.

Kyle said in his email:
If you have the DataMart Client installed and it appears to be functioning
correctly, please let me know and I will notify the DSSNI team that you
have everything in place to respond to the Initial Basic Query against the
CDM.

Ashok and Laurel - did the DSSNI team send the request to you with the
queries attached or did you download the queries and submit the query
request to your datamart?



Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Mon, Feb 9, 2015 at 10:20 AM, Verhagen, Laurel A 
verhagen.lau...@mcrf.mfldclin.edu wrote:

  Ashok,



 I have the same problem with the SQL server version that I’m trying to
 run. Sent an email to Jessica, but apparently the HPHCI offices are closed
 today due to weather.



 Thanks,
 Laurel



 *From:* Mudgapalli, Ashok [mailto:ashok.mudgapa...@unmc.edu]
 *Sent:* Monday, February 09, 2015 10:15 AM
 *To:* Verhagen, Laurel A; Justin Dale

 *Cc:* gpc-dev@listserv.kumc.edu
 *Subject:* RE: PopMedNet node at UNMC



 If that is normal behavior, follow-up issue is …  I got the query file
 downloaded (zip file) and try to unzip, I am not able to unzip I tried many
 ways to unzip), the system says that the *.zip is invalid.  The file is
 oracle based query. Thanks.



 Ashok



 *From:* Verhagen, Laurel A [mailto:verhagen.lau...@mcrf.mfldclin.edu
 verhagen.lau...@mcrf.mfldclin.edu]
 *Sent:* Monday, February 09, 2015 9:52 AM
 *To:* Justin Dale; Mudgapalli, Ashok
 *Cc:* gpc-dev@listserv.kumc.edu
 *Subject:* RE: PopMedNet node at UNMC



 Justin is correct. Instructions are to download the queries, run locally,
 then upload. This is different than the first connectivity test.



 Thanks,
 Laurel



 *From:* gpc-dev-boun...@listserv.kumc.edu [
 mailto:gpc-dev-boun...@listserv.kumc.edu
 gpc-dev-boun...@listserv.kumc.edu] *On Behalf Of *Justin Dale
 *Sent:* Monday, February 09, 2015 9:41 AM
 *To:* Mudgapalli, Ashok
 *Cc:* gpc-dev@listserv.kumc.edu
 *Subject:* Re: PopMedNet node at UNMC



 We're seeing same screen when trying to edit the data model settings.
 I'm wondering if this is the intended behavior since these are all file
 distribution queries and we're supposed to open the file and run against
 the CDM through whichever mechanism we choose and then attach the results
 to the request?  Not sure about all of this - suggest discussing in
 tomorrow's call.



 [image: Inline image 1]


Regards,



 Justin Dale

 Manager - Research Development and Support

 University of Minnesota

 Academic Health Center - Office of Information Systems

 Phone: 612.624.9747

 Fax: 612.624.7458

 jd...@umn.edu



 On Mon, Feb 9, 2015 at 9:14 AM, Mudgapalli, Ashok 
 ashok.mudgapa...@unmc.edu wrote:

 We were able install the Popmednet 5.0 version of the data mart client and
 connect to the PCORnet network.  We are able to receive the
 “file distribution” query into our Data Mart client but unable to configure
 local Data Mart to execute the query for following reason. If you happen to
 know the solution or came across this issue please let me know. I sent an
 email to support team and waiting for the response.

 My local data mart is on Oracle.

 I did as follows:

 DataMart Client à Settings - Edit à highlighted our DataMart
 (C4-University of Nebraska Medical … à Edit à DataMart Settings dialog
 has

  Clicked on Edit and it showed no model processor.











 Ashok Mudgapalli, MS, Ph.D.

 Director of Research IT (Vice Chancellor for Research Office)

 Assistant Professor

 Genetics, Cell Biology, and Anatomy

 College of Medicine

 University of Nebraska Medical Center

 Omaha, NE 68198-7878

 402-559-9072




 The information in this e-mail may be privileged and confidential,
 intended only for the use of the addressee(s) above. Any unauthorized use
 or disclosure of this information is prohibited. If you have received this
 e-mail by mistake, please delete it and immediately contact the sender.


 ___
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 Gpc-dev@listserv.kumc.edu
 http://listserv.kumc.edu/mailman/listinfo/gpc-dev


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Re: PopMedNet node at UNMC

[Justin Dale]

We're seeing same screen when trying to edit the data model settings.   I'm
wondering if this is the intended behavior since these are all file
distribution queries and we're supposed to open the file and run against
the CDM through whichever mechanism we choose and then attach the results
to the request?  Not sure about all of this - suggest discussing in
tomorrow's call.

[image: Inline image 1]

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Mon, Feb 9, 2015 at 9:14 AM, Mudgapalli, Ashok ashok.mudgapa...@unmc.edu
 wrote:

   We were able install the Popmednet 5.0 version of the data mart client
 and connect to the PCORnet network.  We are able to receive the
 “file distribution” query into our Data Mart client but unable to configure
 local Data Mart to execute the query for following reason. If you happen to
 know the solution or came across this issue please let me know. I sent an
 email to support team and waiting for the response.

 My local data mart is on Oracle.

 I did as follows:

 DataMart Client à Settings - Edit à highlighted our DataMart
 (C4-University of Nebraska Medical … à Edit à DataMart Settings dialog
 has

  Clicked on Edit and it showed no model processor.











 Ashok Mudgapalli, MS, Ph.D.

 Director of Research IT (Vice Chancellor for Research Office)

 Assistant Professor

 Genetics, Cell Biology, and Anatomy

 College of Medicine

 University of Nebraska Medical Center

 Omaha, NE 68198-7878

 402-559-9072



 The information in this e-mail may be privileged and confidential,
 intended only for the use of the addressee(s) above. Any unauthorized use
 or disclosure of this information is prohibited. If you have received this
 e-mail by mistake, please delete it and immediately contact the sender.

 ___
 Gpc-dev mailing list
 Gpc-dev@listserv.kumc.edu
 http://listserv.kumc.edu/mailman/listinfo/gpc-dev


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Re: More info for the GPC BC Search (encounter for each tumor of each patient)

[Justin Dale]

Thanks for sharing this.  At UMN we were not taking into account multiple
tumors per patient and thus only had one encounter per patient in i2b2 for
the tumor registry patients.  We going to refactor our code and reload the
data for this prior to running the BC cohort.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu

On Thu, Jan 8, 2015 at 9:16 AM, Dan Connolly dconno...@kumc.edu wrote:

 The fabricated visit won't distinguish among multiple tumors found in one
 patient. If that case doesn't occur in your data set, very well. But
 otherwise, that's a significant problem.

 The HERON ETL code uses a combination of (per-patient) accession number
 and sequence number to identify a tumor registry encounter:

 341 create or replace view tumor_reg_visits as
 342 select ne.Accession Number--Hosp || '-' || ne.Sequence
 Number--Hospital
 343as encounter_ide
 344  , ne.Patient ID Number as MRN
 345 from naacr.extract ne
 346 where ne.Accession Number--Hosp is not null;

 ref
 https://informatics.kumc.edu/work/browser/heron_load/naaccr_txform.sql#L341

 p.s. Note Tamara, Betsy, myself, and others discussed this specific case
 of handling multiple tumors per patient Aug 29.
 https://informatics.gpcnetwork.org/trac/Project/ticket/32#comment:27

 p.p.s. I presume it's OK to bring this technical discussion back to the
 mailing lists (and, consequently, share it  publicly). It's important that
 we all learn together.

 --
 Dan

 
 From: Tamara McMahon
 Sent: Wednesday, January 07, 2015 4:39 PM
 To: 'Bushee, Glenn'
 Cc: Dan Connolly
 Subject: RE: More info for the GPC BC Search

 Glenn,

 They want data for every element in the search when available.  The
 financial encounter is based on the encounter number attached to the tumor
 registry observance.  I believe this is the tumor number (copying Dan to
 verify).

 Data update through 10/28/2014 is great.  It covers the desired BC date
 range.

 -Original Message-
 From: Bushee, Glenn [mailto:gbus...@mcw.edu]
 Sent: Tuesday, January 06, 2015 2:46 PM
 To: Tamara McMahon
 Subject: Re: More info for the GPC BC Search

 Tamara, the financial encounter constraint is a difficult one on our end.
 We've pulled data from 3 different NAACCR databases and used the fabricated
 visit (EPIC Zid preceded by 'fabricated_') for all of the entries.  So,
 this would mean that our query is currently taking any SEER Site: Breast,
 excluding any match to the Class of Case = 30.  Note that this exclusion
 reduces our data set size by about a 150 patient count.

 For the extracted data, is it that you just want the information
 associated with the SEER Site: Breast entry?

 So, the next question is then, how are you determining a Financial
 Encounter from the underlying NAACCR data?

 I hope that this all makes sense.

 We received a one-time data dump that was through approximately
 10/28/2014.  We are going to be working through a process to obtain
 incremental changes on either a monthly or quarterly basis, but this has
 not been finalized yet.

 - Glenn

Medical Informatics Senior Analyst
CTSI – Clinical  Translational Science Institute
gbus...@mcw.edu
(414) 805-7239


 From: Tamara McMahon tmcma...@kumc.edumailto:tmcma...@kumc.edu
 Date: Tuesday, January 6, 2015 at 2:16 PM
 To: 'gpc-honest-brok...@listserv.kumc.edumailto:'
 gpc-honest-brok...@listserv.kumc.edu' 
 gpc-honest-brok...@listserv.kumc.edumailto:
 gpc-honest-brok...@listserv.kumc.edu
 Cc: Chrischilles, Elizabeth A (e-chrischil...@uiowa.edumailto:
 e-chrischil...@uiowa.edu) e-chrischil...@uiowa.edumailto:
 e-chrischil...@uiowa.edu, McDowell, Bradley D (
 bradley-mcdow...@uiowa.edumailto:bradley-mcdow...@uiowa.edu) 
 bradley-mcdow...@uiowa.edumailto:bradley-mcdow...@uiowa.edu, Theresa
 Shireman tshire...@kumc.edumailto:tshire...@kumc.edu, Jianghua He 
 j...@kumc.edumailto:j...@kumc.edu
 Subject: More info for the GPC BC Search

 I would like to clarify a few items in the previous email regarding GPC
 Breast Cancer search. I’ve attached an updated screenshot highlighting
 items listed below.

 1.   The first 3 groups should be limited to the same financial
 encounter.  When I printed the query, the printout indicated treat
 independently which is incorrect.  Please refer to the correct query
 (attached).

 2.   Group 2 excludes non-analytic class of case.  Analytic class of
 case is less than 30, so please exclude any class of case greater or equal
 to 30 to remove the non-analytics.  The query print I am attaching shows
 the non-analytic class of case codes available at KUMC.  You may see
 different numbers at your institution.  For example, KUMC is missing #35,
 #37 and #39.  Your institutions may include these but miss some of those
 listed in the KUMC search. The important thing

Cancer Identification\Primary Site VS SEER Site Summary

[Justin Dale]

Can someone provide insight on the differences between the Primary Site
under Cancer Identification vs SEER Site Summary?

For example, the breast has nine corresponding ICD-0-3 sites (C500-C509),
all of which are listed under Cancer Identification  Primary Site  Breast
in KUMC's babel hierarchy.  I can select the individual sites or the entire
folder to include all sites.  Under the SEER Site Summary in KUMC's babel
hierarchy, Breast is listed with a recode of 26000, which I assume rolls up
the nine site codes based on info from the SEER website (
http://seer.cancer.gov/siterecode/icdo3_d01272003/).

I'm having difficulty understanding the differences between the two and is
it really necessary to implement the SEER Site Summary in our i2b2.  Does
it have to do with a point in time in which ICD-0 was implemented and the
SEER site summary was how it used to be done?

Your insights are much appreciated. Thanks.

Justin
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Re: I2B2 demos next week

[Justin Dale]

UMN's offer is still good.

Justin


On Mon, Apr 7, 2014 at 10:45 AM, Verhagen, Laurel A 
verhagen.lau...@mcrf.mfldclin.edu wrote:

  Marshfield update: We are working on the population increase this week.
 There was a minor delay with upgrading from v1.5 to v1.6. We still have a
 few ontology quirks to resolve, so likely would postpone a demo for a few
 weeks.



 Thanks,

 Laurel



 *From:* gpc-dev-boun...@listserv.kumc.edu [mailto:
 gpc-dev-boun...@listserv.kumc.edu] *On Behalf Of *Dan Connolly
 *Sent:* Monday, April 07, 2014 10:38 AM
 *To:* GPC-DEV@LISTSERV.KUMC.EDU
 *Subject:* RE: I2B2 demos next week



 Resuming this discussion...

 Hubert, ready to show us what you've got at UNMC?

 Justin, is your offer still good re UMN?

 Failing that...

 Nate, though not directly related to CMH, is there anything you can demo
 for us?

 Laruel, is Marshfield out of the woods with those update problems?

 --
 Dan

   --

 *From:* Greater Plains Collaborative Software Development [
 GPC-DEV@LISTSERV.KUMC.EDU] on behalf of Justin Dale [jd...@umn.edu]
 *Sent:* Wednesday, February 05, 2014 8:56 AM
 *To:* GPC-DEV@LISTSERV.KUMC.EDU
 *Subject:* Re: I2B2 demos next week

 Ok, we'll do it.






 On Tue, Feb 4, 2014 at 5:55 PM, Campbell, James R campb...@unmc.edu
 wrote:

 Minnesota, you are up as Hubert has the platform working but we have
 precious little data yet

 Jim



 *From:* Greater Plains Collaborative Software Development [mailto:
 GPC-DEV@LISTSERV.KUMC.EDU] *On Behalf Of *Dan Connolly
 *Sent:* Tuesday, February 04, 2014 1:20 PM
 *To:* GPC-DEV@LISTSERV.KUMC.EDU


 *Subject:* I2B2 demos next week



 I neglected to solicit volunteers in the teleconference, so...

 Python 2.7.3 (default, Sep 26 2013, 20:03:06)
  sites = set(['kumc', 'cmh', 'Iowa', 'wisc', 'mcw', 'mcrf', 'umn',
 'unmc', 'uthscsa', 'utsw'])
  recent = ['utsw', 'kumc']
  candidates = sites - set(recent)
  from random import sample
  nominations = sample(candidates, len(candidates))
  nominations
 ['unmc', 'uthscsa', 'umn', 'cmh', 'mcrf', 'Iowa', 'mcw', 'wisc']

 Hubert and UNMC folks, can you give a taste of what you've got so far
 after just a few weeks?

 Alex, John, Alfredo, likewise, would you please show us what's cooking so
 far at UTHSCSA?

 Otherwise, please let the next in line know that they're nominated.

 --
 Dan


 The information in this e-mail may be privileged and confidential,
 intended only for the use of the addressee(s) above. Any unauthorized use
 or disclosure of this information is prohibited. If you have received this
 e-mail by mistake, please delete it and immediately contact the sender.


--
 The contents of this message may contain private, protected and/or
 privileged information. If you received this message in error, you should
 destroy the e-mail message and any attachments or copies, and you are
 prohibited from retaining, distributing, disclosing or using any
 information contained within. Please contact the sender and advise of the
 erroneous delivery by return e-mail or telephone. Thank you for your
 cooperation.

 ___
 Gpc-dev mailing list
 Gpc-dev@listserv.kumc.edu
 http://listserv.kumc.edu/mailman/listinfo/gpc-dev


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Clarity notes question

[Justin Dale]

Does anyone extract notes from Clarity which maintain the original format
(eg. RTF or HTML)?  The notes in the HNO_NOTE_TEXT table have been
converted to plain--text and have all formatting removed (even line
breaks).  Maybe there is another Clarity table that would maintain the
original format? Or maybe its a configuration setting within the Cache 
Clarity load?

I realized this question is outside the current GPC scope but figured it
wouldn't hurt to ask.

Thanks for your responses.

Justin
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Re: I2B2 demos next week

[Justin Dale]

Ok, we'll do it.




On Tue, Feb 4, 2014 at 5:55 PM, Campbell, James R campb...@unmc.edu wrote:

  Minnesota, you are up as Hubert has the platform working but we have
 precious little data yet

 Jim



 *From:* Greater Plains Collaborative Software Development [mailto:
 GPC-DEV@LISTSERV.KUMC.EDU] *On Behalf Of *Dan Connolly
 *Sent:* Tuesday, February 04, 2014 1:20 PM
 *To:* GPC-DEV@LISTSERV.KUMC.EDU

 *Subject:* I2B2 demos next week



 I neglected to solicit volunteers in the teleconference, so...

 Python 2.7.3 (default, Sep 26 2013, 20:03:06)
  sites = set(['kumc', 'cmh', 'Iowa', 'wisc', 'mcw', 'mcrf', 'umn',
 'unmc', 'uthscsa', 'utsw'])
  recent = ['utsw', 'kumc']
  candidates = sites - set(recent)
  from random import sample
  nominations = sample(candidates, len(candidates))
  nominations
 ['unmc', 'uthscsa', 'umn', 'cmh', 'mcrf', 'Iowa', 'mcw', 'wisc']

 Hubert and UNMC folks, can you give a taste of what you've got so far
 after just a few weeks?

 Alex, John, Alfredo, likewise, would you please show us what's cooking so
 far at UTHSCSA?

 Otherwise, please let the next in line know that they're nominated.

 --
 Dan


 The information in this e-mail may be privileged and confidential,
 intended only for the use of the addressee(s) above. Any unauthorized use
 or disclosure of this information is prohibited. If you have received this
 e-mail by mistake, please delete it and immediately contact the sender.

Re: https://redcap.kumc.edu/surveys/?s=mpps4H file not loading

[Justin Dale]

I experienced the same issue when uploading an 18MB csv.  I compressed it
to about 2MB and then it worked fine.

We're big fans of Google drive here at Minnesota.

Regards,

Justin Dale
Manager - Research Development and Support
University of Minnesota
Academic Health Center - Office of Information Systems
Phone: 612.624.9747
Fax: 612.624.7458
jd...@umn.edu


On Wed, Jan 22, 2014 at 12:33 PM, Dan Connolly dconno...@kumc.edu wrote:

  Well, I just tested it on a trivial file and it worked OK.

 But for the actual terms from KUMC HERON, the max upload size is too
 small, so we cheated and scp'd the data. I'm happy to give ssh access to
 anybody who sends me a public key.

 I'd be surprised if an email attachment would work, but you're welcome to
 try. (to me only; don't send it to the list)

 I'm open to other options too:

- dropbox
- google drive
- ...?


  --
 *From:* Greater Plains Collaborative Software Development [
 GPC-DEV@LISTSERV.KUMC.EDU] on behalf of Wilson Nathan [
 nwil...@uwhealth.org]
 *Sent:* Wednesday, January 22, 2014 11:56 AM
 *To:* GPC-DEV@LISTSERV.KUMC.EDU
 *Subject:* https://redcap.kumc.edu/surveys/?s=mpps4H file not loading

   All

 Is 
 *https://redcap.kumc.edu/surveys/?s=mpps4H*https://redcap.kumc.edu/surveys/?s=mpps4Hhaving
  any issues?
 It doesn’t seem to upload my file.  I get the uploading screen and it just
 spins.

 I’ve tried three different times today with no luck.

 Nathan


 *Nathan S. Wilson*
 Ontologist
 Health Information Management Center (HIMC)

 *__*
 301 S. Westfield Rd - Suite 320
 Madison, WI  53717
 Phone: (608) 890-5780
 eMail: nwil...@uwhealth.org