Is the version of the SCILHS ontology observable across sites? Perhaps it is, but I'd like to figure out exactly how so it's clear what choosing a particular version would entail. Our decision is "using a common approach" (Apr 25 #160<https://informatics.gpcnetwork.org/trac/Project/ticket/160#comment:24>). There has been considerable adaptation of the approach at each site; our decision so far doesn't bind us to any particular version of the i2p-transform code nor the SCILHS ontology.
We (GPC) are using it to build CDM DataMarts at each site... and for Breast Cancer diagnoses and procedures, we're sharing data from CDM tables across sites. So if SCILHS changed their ontology, it's possible it would be visible via that process. But I can't put my finger on any particular way. At KUMC, we grabbed the version as of Feb 22<https://github.com/njgraham/scilhs-ontology/commit/527c0879e1adf5272002c50452aabfb16d89d1e3>, which seems to be 1.5.2. Our branch<https://github.com/njgraham/scilhs-ontology> is at e81dc25, "11 commits ahead, 78 commits behind SCILHS:master." We should probably merge those 78 commits, but we haven't run into anything that would prompt us to do so. Looking at their CHANGELOG<https://github.com/SCILHS/scilhs-ontology/blob/master/CHANGELOG.md>... v2.02 and v2.03 changes seem to be in labs and meds, but our adaptation of the i2p-transform code involves more or less replacing their labs and meds ontologies with our own, using pcori_basecode as a mapping. Ah... this could be noticeable: * Developed update script to add new CDM v3.0 fields to encounter, diagnosis, and vitals tables. -- Dan ________________________________ From: Campbell, James R [[email protected]] Sent: Sunday, August 28, 2016 6:22 AM To: Dan Connolly; McClay, James C Cc: [email protected]; Brittany Zschoche Subject: RE: SCILHS i2b2 ontology [was: 8.24.16 GPC Site PM Notes] Dan I raised the question as to what metadata standard we re going to use within GPC to support GPC and PCORI network i2b2 interface queries between sites. I understood that we would be using SCILHS and we are installing SCILHS 2.02 that I got from Jeff Klann. However I did not hear a unanimous response from all GPC sites and some were relating that they were using earlier versions of JK's code used to extract CDMV3 from SCILHS. UNMC is extracting CDMV3 directly from our standards-based i2b2 metadata but we want to be team players and also install i2b2 metadata that will allow us to respond to GPC queries from i2b2. So I am asking for a stake-in-the-sand agreement among our net collaborators as to what metadata we will all deploy for that purpose, and if SCILHS - are we agreeing on 2.02? Jim ________________________________ From: Dan Connolly [[email protected]] Sent: Friday, August 26, 2016 3:08 PM To: McClay, James C; Campbell, James R Cc: [email protected]; Brittany Zschoche Subject: SCILHS i2b2 ontology [was: 8.24.16 GPC Site PM Notes] What about the ontology, Dr. Campbell? Reminder from March 4<redir.aspx?REF=djVwMB-jeCsqlJANz0wEv6nXq5QSEZdkKlJ9CgtcDBhuYmKYJ9DTCAFodHRwOi8vbGlzdHNlcnYua3VtYy5lZHUvcGlwZXJtYWlsL2dwYy1kZXYvMjAxNnExLzAwMjU5NC5odG1s>: it's best to start the discussion in substance in email, leaving aside the question of whether we'll talk about it on a phone call. If, when you see the agenda come out, you don't see your item on it and you're not satisfied with the email discussion, you can always ask for it to be added. -- Dan ________________________________ From: [email protected] [[email protected]] on behalf of Brittany Zschoche [[email protected]] Sent: Friday, August 26, 2016 1:35 PM To: 'McClay, James C' Cc: [email protected] Subject: RE: 8.24.16 GPC Site PM Notes Thanks, Jim. Dan, please see below. From: McClay, James C [mailto:[email protected]] Sent: Friday, August 26, 2016 12:55 PM To: Brittany Zschoche <[email protected]> Subject: RE: 8.24.16 GPC Site PM Notes Brittany, Dr. Campbell would like to put a discussion of SCILHS i2b2 ontology on the GPC-DEV call this Tuesday. jm 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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