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

st 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, 20

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

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

CDM encounter types and CDM refresh

etween refreshes. However, at this stage in the game, we are welcoming corrections, so you are free to go ahead and make all needed changes. We have recently sent you a new query per the process laid out by pcori that is due by June 24." Regards, Justin Dale IT Manager, Academic Healt

Re: [gpc-informatics] #473: PCORnet CDMv3 SAS prep-to-research Readiness

Should each GPC site complete appendix B of the memo by this Friday (5/13) and send it directly to Russ? On Wed, May 11, 2016 at 12:29 PM, Russ Waitman wrote: > Yes. > > I have to meet with Rachael Fleurence, the PCORnet program director at > PCORI next week on Wednesday AM so I need some input

Re: PCORnet data characterization calls

ng 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...@um

Re: [gpc-informatics] #473: PCORnet CDMv3 SAS prep-to-research Readiness

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

Re: [gpc-informatics] #473: PCORnet CDMv3 SAS prep-to-research Readiness

Thanks for the quick responses. One more question if you don't mind: Must I submit the zip file through the DataMart client or is there a way to attach the file to the request within https://querytool.pcornet.org? Regards, Justin Dale Manager - Research Development and Support Universi

Re: [gpc-informatics] #473: PCORnet CDMv3 SAS prep-to-research Readiness

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

Re: gpc-dev 16 Feb agenda and meeting notes

Related to #6, I would like to discuss how/why the UMN breast cancer cohort had dates shifted twice. This is related to ticket 470: https://informatics.gpcnetwork.org/trac/Project/ticket/470 On Mon, Feb 15, 2016 at 1:22 PM, Dan Connolly wrote: > What else for tomorrow? > >- 16 Feb gpc-dev

Geocoding narrative

Attached is the narrative provided by the UMN population center describing the geocoding process for each of the GPC sites back in October. Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone

Re: UMN Q3 quality results in the GPC REDCap database.

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

final enrollment counts for UMN

M. when he cleared those out. Tried that again but still getting errors. Any ideas or help would be appreciated. We generated the csv using Nathan's SQL code (re: ticket #97). Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Cen

Re: [gpc-informatics] #350: geocoding: distribute census, ACS data to sites

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 > ---+ > Re

Re: #350 geocoding: distribute census, ACS data to sites

) and email addresses who will be responsible for downloading the files? I will move the files into the appropriate folders and then share accordingly. 1. CMH - 2. KUMC - 3. MCRF- 4. MCW - 5. MU - 6. UNMC - 7. UTHSCSA - 8. UTSW - 9. WISC - Thanks. Regards, Justin Dale

Re: gpc-dev 6 Oct agenda and meeting notes

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 wrote: >

Re: flowsheets in i2b2

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 Universi

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

hanks. 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 wrote: > #329: UMN cancer tumor

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 e

Re: [gpc-informatics] #174: federated login for GPC data store

Very cool! I just logged in using my UMN credentials. 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, Apr 30, 2015 at 1:28 PM, GPC

Re: GPC-Dev Agenda 4-21

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 wrote: > Wisconsin

Re: PopMedNet node at UNMC

uests. 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 Suppor

Re: PopMedNet node at UNMC

tegrate 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, Mudgapall

Re: PopMedNet node at UNMC

itial 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 Minnesot

Re: PopMedNet node at UNMC

hen 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

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

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

UMN - updated ontology for babel

At UMN we've updated our medication ontology to be AUI-based and also have our tumor registry data included. What is the best way to share the csv file to get it reloaded in babel? Re: https://informatics.gpcnetwork.org/trac/Project/ticket/172 Regards, Justin Dale Manager - Res

Re: Cancer Identification\Primary Site VS SEER Site Summary

Thank you Dan, this is very helpful! 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, Aug 22, 2014 at 5:53 PM, Dan Connolly wrote: >

Cancer Identification\Primary Site VS SEER Site Summary

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.

updated UMN i2b2 ontologies for babel

de it once complete but it slipped through the cracks. We'll hopefully have another revision shortly that will contain our tumor registry and flowsheet data as well. Nathan or Dan, can you load this into babel? Thanks. Regards, Justin Dale Manager - Research Development and Support Uni

Re: NAACCR queries

e the data loaded into i2b2 (yet) I think we can still use the data in its current form to run the queries and to get back counts. Regards, Justin Dale Manager - Research Development and Support University of Minnesota Academic Health Center - Office of Information Systems Phone: 612.624.974

Re: NAACCR queries

; Laurel > > -- > > Laurel Verhagen > > Biomedical Informatics Research Center > > Marshfield Clinic Research Foundation > > 715-221-6433 > > > > *From:* gpc-dev-boun...@listserv.kumc.edu [mailto: > gpc-dev-boun...@listserv.kumc.edu] *On Beha

NAACCR queries

At Minnesota, we now have the NAACCR data loaded into our repository. I believe there were talks about doing some "pen-and-paper" query across sites who have this data available. If this is still an option we would really like to participate. Justin Dale Manager - Research Devel

Re: Boston i2b2

Supreet Kathpalia and Tim Meyer from Minnesota will be attending. 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 16, 2014 at 11:45 AM

Re: I2B2 demos next week

gt; > 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 Developmen

Re: [gpc-informatics] #93: federated login using InCommon for GPC services such as babel

In order to use the University of Minnesota's common login (and avoid another username/password to remember), we setup four parameters for each user within the i2b2 PM cell: 1. authentication_method (our custom method is called UMN but a new one could be added for another location) 2. authenticati

Clarity notes question

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

PCORNet Common Data Model question

I'm reviewing the common data model document and trying to understand how it relates to the GPC. Is this the suggested model for the database that will store the aggregated de-identified data that each site sends back to a central location (figure 1.1 in the proposal)? Regards, Justin

Re: [Gpc-dev] de-identification - patients under 1 year old

pediatricians (or other users)? We currently use a date shift between -1 and -365 days but I'm thinking that may be too extreme. 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

[Gpc-dev] de-identification - patients under 1 year old

Seeking input on how your site represents a patient's age who is under 1 year old? Do you group them in the 1 year old bucket (similar to 90 and over)? Do you provide fractions of a year or represent months (seems like it goes against the safe harbor rules)? Do you shift the birthdate and just pr

Determine where specific data is located inside Clarity

FYI http://www.ehrreporting.com/2010/07/determine-specific-data-locate-inside-clarity/

GPC and i2b2

gies, send that data to KU who will act as the "hub", and have one version of i2b2 for the entire GPC network? At Minnesota we'll soon be implementing medications into i2b2 and I'm trying to understand how that impacts our commitments to the GPC. Thanks for you responses.

Re: I2B2 demos next week

Ok, we'll do it. On Tue, Feb 4, 2014 at 5:55 PM, Campbell, James R 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 Beha

Re: Introductions: role, background, contact info

Thank you for the introduction Dan. I would like to take a moment to introduce the informatics team from the University of Minnesota (UMN) and provide a little background on the Academic Health Center Information Exchange (AHC IE): *Justin Dale - IT Manager, Systems Architect* Leads team of

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

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 - Offi