When I asked for date difference I was asking about any lab type. Glucose labs are not in PCORNET model and have to be pull out from i2b2 separately. For A1c(which is in PCORNET model) I was assuming all sites have all 3 dates available. I was not aware situation is so bad. Lets discuss it in the next CAPRICORN/GPC meeting.
On Wed, Jan 25, 2017 at 12:45 PM, Dan Connolly <dconno...@kumc.edu> wrote: > I started looking at date differences... for similar reasons to the ones > Alex gave, I thought a histogram was in order... I had assumed the specimen > date and order date were in the same table as the result date. But I don't > see them. I don't know where they are. > > My earlier 1 to 2 month estimate for revising HERON ETL was based on this > assumption. I no longer have a clear design in my head, so multiply my > estimate by 2x to 3x until I know more. > > -- > Dan > > ________________________________________ > From: Gpc-dev [gpc-dev-boun...@listserv.kumc.edu] on behalf of Stoddard, > Alexander [astodd...@mcw.edu] > Sent: Wednesday, January 25, 2017 11:41 AM > To: gpc-dev@listserv.kumc.edu > Subject: Re: [gpc-informatics] #551: next-D labs for cohort selection > > I’ll return the Excel spreadsheet survey with info for MCW outside of the > dev list. > > MCW uses RESULT_DATE for the i2b2 “START_DATE” for lab facts. START_DATE > being a very poor name imposed by the i2b2 schema, it’s really just “some > date” for a fact without any explicit context – hence the difference > choices we will find between sites. It is also the “only date” that can be > used to ask time relative questions of any given set of facts in i2b2 > unless we start creating related concepts or being inventive with modifier > codes. I know of no example of i2b2 modifier codes modifying the _date_ of > a fact as opposed to the _value_. I think the schema would support it in > principle but I have no idea if the client and generated queries would. > This would also be a long term major ETL development task. > > We do have all three of order_date, specimen_date and result_date from our > Epic source data. But specimen date is only partially available, we are at > the mercy of manual data entry and data validation upstream of us in the > system. That is, at least in part, why MCW made the expedient choice of > making RESULT_DATE our anchor for lab facts, it was the “best” one that was > consistently available in the large. > > Are the max difference questions for the different date types to be > answered in the limited context of only to A1C values, or all lab results > in our source system (or some broader subset)? > > I fear a simple max difference is going to be non-robust, uninformative, > and look very bad (or even nonsensical) for us. Some work flows upstream > (at least at MCW) for entering lab results into the EHR use manual data > abstraction, and others use (at times broken) automated abstraction with > poorly mapped date field semantics. There is going to be some percentage of > completely bogus date values. To truly assess the lag between the different > lab date semantics will probably take calculating percentiles of the > differences for individual lab tests – this is obviously more effort and we > will need guidance on how soon an answer is needed for it to be useful and > if it is worth the effort and/or worth the wait. > > Thank you, > > Alex Stoddard > Biomedical Informatics Software Engineer > CTSI > Medical College of Wisconsin > > > > Date: Wed, 25 Jan 2017 08:29:17 -0600 > From: "Al'ona Furmanchuk" <furmanc...@icnanotox.org> > To: Dan Connolly <dconno...@kumc.edu> > Cc: Bernard Black <bbl...@kellogg.northwestern.edu>, > "<gpc-dev@listserv.kumc.edu>" <gpc-dev@listserv.kumc.edu> > Subject: Re: [gpc-informatics] #551: next-D labs for cohort selection: > fasting glucose, HbA1c > Message-ID: > <CADEvUy6gXhN009NApqYucrnjUkds1zODzPW6fwyOVRk7cY964A@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Before we go toward changes, lets just see if we need to. I would > appreciate if each site could fill up attached form and send back to > me. I > filled some sites based on this discussion. Please, check and correct > if I > got it wrong. > Alona. > > > > _______________________________________________ > Gpc-dev mailing list > Gpc-dev@listserv.kumc.edu > https://urldefense.proofpoint.com/v2/url?u=http-3A__ > listserv.kumc.edu_mailman_listinfo_gpc-2Ddev&d=CwIF-g&c= > yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=- > aRkmw3Ob1oZRrrYmR1wHysw9FWMRlmk_CMIVWKi32KhS_EbXW7cMBGcBAmqh95W&m= > mAT174c22jd9Dp-j2U1wODN8ACYRPI5Th5s_WY-HWS8&s=B-0vV1or45x1npbgh4- > mQuDtqI1g8PORJWvYsJkN9Ic&e= > -- Al’ona Furmanchuk, Ph.D. Research Associate Department of Electrical Engineering and Computer Science Northwestern University 2145 Sheridan Road, Tech L359 Evanston, IL 60208 Web: http://furmanchuk.com/ E-mail: alona.furmanc...@northwestern.edu <furmanc...@icnanotox.org> Phone: 847-467-2299
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