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 [email protected] On Thu, Jan 8, 2015 at 9:16 AM, Dan Connolly <[email protected]> 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" > 343 as 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:[email protected]] > 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 > [email protected] > (414) 805-7239 > > > From: Tamara McMahon <[email protected]<mailto:[email protected]>> > Date: Tuesday, January 6, 2015 at 2:16 PM > To: "'[email protected]<mailto:' > [email protected]>'" < > [email protected]<mailto: > [email protected]>> > Cc: "Chrischilles, Elizabeth A ([email protected]<mailto: > [email protected]>)" <[email protected]<mailto: > [email protected]>>, "McDowell, Bradley D ( > [email protected]<mailto:[email protected]>)" < > [email protected]<mailto:[email protected]>>, Theresa > Shireman <[email protected]<mailto:[email protected]>>, Jianghua He < > [email protected]<mailto:[email protected]>> > 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 is to exclude any class of > case coded greater than or equal to 30. > > 3. I’ve added 0610 Class of Case to group 3, so the team can verify > non-analytics were removed. > > 4. I pulled the EMR data types into the 4th group since they cannot > be linked via financial encounter at KUMC. > > Please email me and let me know the date of your last data refresh and > what kind of lag exists for your tumor registry. Due to the close date > range (identified 5/1/2013-5/1/2014) the BC team would like to verify the > availability of this data. At KUMC we refresh monthly with a lag of 6 > months at the registrar, so our tumor registry is only available through > 6/30/2014. > > Reminder: please include a de-identified patient number in your data set. > > Dan is working on ticket #205< > https://informatics.gpcnetwork.org/trac/Project/ticket/205>: an interim > data builder for this search. I will send an update on how to pull/package > the data from the search once I get an update from him. > > Tamara McMahon > Clinical Informatics Coordinator > Division of Medical Informatics > University of Kansas Medical Center > 913-945-7470 > Request a training or consultation< > https://redcap.kumc.edu/surveys/?s=qYxMmb> > > _______________________________________________ > Gpc-dev mailing list > [email protected] > http://listserv.kumc.edu/mailman/listinfo/gpc-dev >
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