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projects:workgroups:phenotyping [2014/11/19 14:07] jbanda created |
projects:workgroups:phenotyping [2015/09/15 16:43] jbanda |
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- | **Objectives:** | + | **Objective:** |
- | **Project Leads:** [[http://ohdsi.org/who-we-are/collaborators/martijn-schuemie/|Martijn Schuemie, PhD]],[[http://ohdsi.org/who-we-are/collaborators/marc-suchard/|Marc Suchard, MD, PhD]] | + | To build and evaluate a computational pipeline for electronic phenotyping -- which defines criteria to algorithmically select sets of patients based on stored clinical data -- in the OHDSI project. Our approach for learning statistical models of clinical phenotypes is called XPRESS, which stands for eXtraction of Phenotypes from clinical REcords using Silver Standards. |
+ | **Project Leads:** | ||
+ | [[http://ohdsi.org/who-we-are/collaborators/nigam-shah/|Nigam Shah, MBBS, PhD]] | ||
**The plan:** | **The plan:** | ||
- | * Jan 2015: final XPRESS pipeline ready | + | * Jan 2015: final XPRESS pipeline ready |
- | * March 2015: 10 models built | + | * March 2015: 10 models built |
- | * May 2015: Test portability of 10 models | + | * May 2015: Test portability of 10 models |
- | * July 2015: Run the XPRESS vs. “queries” comparison at a non-stanford site. | + | * July 2015: Run the XPRESS vs. “queries” comparison at a non-stanford site. |
- | * Oct 2015: Decide the approach to use in OHDSI | + | * Oct 2015: Decide the approach to use in OHDSI |
- | **Levels of membership/commitment:** | + | **The Participants:** |
- | * Prioritizing the list of phenotypes to build models for | + | * Juan Banda |
- | * Apply a trained model at your site and assess performance (i.e. examine portability) | + | * Vibhu Agarwal |
- | * Run the XPRESS pipeline, and build models for a set of phenotypes. | + | * George Hripsack (+ Barnett Chiu, Sunny Chang) |
- | * Get in the guts of the pipeline, mess with feature engineering, etc. | + | * Nicholas Tatonetti (+ Alexandre Yahi) |
- | * Try different approaches (models for episodic events) | + | * Jon Duke (+ Saeed Malas) |
- | + | ||
- | **The commitments (all tentative, please think about finalizing):** | + | |
- | + | ||
- | **George Hripsack (+ Barnett Chiu, Sunny Chang):** | + | |
- | * Apply a trained model from other sites. | + | |
- | * Run XPRESS for new phenotypes. | + | |
- | + | ||
- | **Nicholas Tatonetti (+ Alexandre Yahi)** | + | |
- | * Prioritizing phenotypes | + | |
- | * Applying a trained model from other sites | + | |
- | + | ||
- | **Jon Duke (+ need name)** | + | |
- | * Apply a trained model from other sites | + | |
- | * Run XPRES to build new models | + | |
- | + | ||
- | **[thinking about availability]** | + | |
- | * Tiffany Callahan (UC Denver, biostats) | + | |
- | * Daniella Meeker (Cheryl Chiu) | + | |
**Start Date:** January 2015. | **Start Date:** January 2015. | ||
- | **Repository:** TBD | + | **Repository:** https://github.com/OHDSI/Aphrodite |
**WG Minutes:** Need to find a good place | **WG Minutes:** Need to find a good place | ||
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==== Meetings ==== | ==== Meetings ==== | ||
- | Schedule: Ad hoc | + | Schedule: Every 2nd week on Thursday • from September 17, 2015 • 9 a.m. PDT / 1 hr |
+ | |||
+ | To join the Meeting: | ||
+ | [[https://bluejeans.com/286365503]] | ||
+ | |||
+ | To join via Browser: | ||
+ | [[https://bluejeans.com/286365503/browser]] | ||
+ | |||
+ | To join with Lync: | ||
+ | [[https://bluejeans.com/286365503/lync]] | ||
+ | |||
+ | To join via Cisco Jabber Video: | ||
+ | [[https://bluejeans.com/286365503/jabber]] | ||
- | Call in Number: Need to add | + | To join via Room System: |
+ | Video Conferencing System: bjn.vc -or- 199.48.152.152 | ||
+ | Meeting ID: 286365503 | ||
- | Attendee access code: Need to add | + | To join via Phone:\\ |
+ | 1) Dial:\\ | ||
+ | +1 408 740 7256\\ | ||
+ | +1 888 240 2560(US Toll Free)\\ | ||
+ | +1 408 317 9253(Alternate Number) - (see all numbers - http://bluejeans.com/numbers) \\ | ||
+ | 2) Enter Conference ID: 286365503 \\ | ||
=== Minutes and Agendas === | === Minutes and Agendas === |