Section outline

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    • Use of Electronic Health Record Data for Research 

      (Click for Course Description)

      EPI 231 Spring 2022 (3 units).

      Course Director: Anobel Odisho, MD, MPH
      Assistant Professor, Department of Urology

    • Reminder:  All students who plan to attend in-person activities on campus must complete the daily health screener:  https://ucsf-clinicalcrm.secure.force.com/UCSFHealthScreening

      Though UCSF Masking Policies may continue to evolve, please continue to wear masks in class (and eat and drink outside of class time) to protect yourself and others.

      COVID Testing Resources:  https://coronavirus.ucsf.edu/testing

    • News Forum
      Not available unless: You belong to a group in Registered Students Only
    • General Forum
      Not available unless: You belong to a group in Registered Students Only
    • Final Project File
    • Submit final project, due Monday June 6th at 5 pm Assignment
      Opened: Thursday, May 26, 2022, 12:00 AM
      Due: Monday, June 6, 2022, 5:00 PM
      Not available unless: You belong to Registered Students Only
    • data dictionary URL

  • Tuesday, March 29, 2022; 8:45 AM - 9:15 AM

    EHR Structure
    How EHR systems work, EHR Data Architecture, and UCSF resources, Intro to Databases and Data Types, SQL.

    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

    • Lecture Slides:

    • Lecture 1 - Intro to Databases and UCSF Data File
    • Lecture 1 (PDF) File

    • Lecture Audio/Video Recording (Access restricted to registered students): 

    • Intro to EHR Data and UCSF Data Sources Media Resource
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Class Recording 2021 Media Resource
      Not available unless: You belong to Registered Students Only

    • Required Reading:

    • Intro to SQL File
    • In-person lecture 2022 URL
      Not available unless: You belong to a group in Registered Students Only
    • DeID Data Dictionary File

  • Tuesday, March 29, 2022; 9:15 AM - 10:15 AM

    Computer Laboratory A
    Access to De-ID Data Warehouse, RAE, and preparation of analytic environment

    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

  • Friday, April 1, 2022; 3:15 PM - 5:00 PM

    Computer Laboratory B
    Access to De-ID Data Warehouse, RAE, and preparation of analytic environment

    Faculty:  Anobel Odisho

  • Tuesday, April 5, 2022; 8:45 AM - 9:15 AM

    Study Design

    Research and study designs with EHR Data

    Faculty:  Mark Pletcher

    Location: Mission Hall MH-1400

    • Lecture Slides:

    • Lecture 2 slides File

    • Lecture Audio/Video Recording (Access restricted to registered students): 

    • Lecture 2 - EHR Research Study Design Media Resource
      Not available unless: You belong to Registered Students Only
    • DCR Lecture – Physiology and Anatomy of Research Media Resource
      Not available unless: You belong to Registered Students Only
    • Study Design Basics Media Resource
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • DRAFT - DCR-5, Chapter 16 - Using Existing Data for Research File
      Not available unless: You belong to Registered Students Only

  • Tuesday, April 5, 2022; 9:15 AM - 10:15 AM

    Computer Laboratory A
    Continue access, environment set up, and basic query.

    Faculty:  Mark Pletcher

    Location: Mission Hall MH-1400

  • Friday, April 8, 2022; 3:15 PM - 5:00 PM

    Computer Laboratory B
    Continue access, environment set up, and basic query.

    Faculty:  Anobel Odisho

  • Tuesday, April 12, 2022; 8:45 AM - 9:15 AM

    Diagnosis and Procedure Data
    Sources of diagnosis data, Diagnosis and Procedure Codes, ICD, CPT, HCPCS, SNOMED, UMLS

    Faculty:   Anobel Odisho

    Location: Mission Hall MH-1400

    • Lecture Slides:

    • Lecture 3 - Diagnoses and Procedures File

    • Lecture Audio/Video Recording (Access restricted to registered students): 

    • Lecture 3 - Diagnoses and Procedures Recording Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

  • Tuesday, April 12, 2022; 9:15 AM - 10:15 AM

    Computer Laboratory A
    Creating cohorts based on encounters and diagnosis codes

    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

    • Assignment Answer Key (Access restricted to registered students):

  • Friday, April 15, 2022; 3:15 PM - 5:00 PM

    Computer Laboratory B
    Creating cohorts based on encounters and diagnosis codes.

    Faculty:  Anobel Odisho

  • Tuesday, April 19, 2022; 8:45 AM - 9:15 AM

    Medications
    Analyzing Medication Data (inpatient, ambulatory, continuous), RxNorm


    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

    • Lecture Slides:

    • Lecture 4 - Medications Slides File
    • Lecture 4 - Medications (SQL Code) File

    • Lecture Audio/Video Recording (Access restricted to registered students): 

    • Lecture 4 - Medications Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

  • Tuesday, April 19, 2022; 9:15 AM - 10:15 AM

    Computer Laboratory A
    Refine cohort based on medication data, and extract med admin data

    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

    • Lab 4 - HTML File
    • Lab 4 - RMD File
    • Submit lab 4, due Monday, April 25 at 5 pm Assignment
      Due: Monday, April 25, 2022, 5:00 PM
      Not available unless: You belong to Registered Students Only

    • Assignment Answer Key (Access restricted to registered students):

    • lab_4_key.html File

  • Friday, April 22, 2022; 3:15 PM - 5:00 PM

    Computer Laboratory B
    Refine cohort based on medication data, and extract med admin data

    Faculty:  Anobel Odisho

  • Tuesday, April 26, 2022; 8:45 AM - 9:15 AM

    Lab Data
    Analysis and extraction of lab and imaging data. LOINC

    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

    • Lecture Slides:

    • Lecture 5 - Labs Slides File
    • Lecture 5 - Labs (Rmd) File
    • Lecture 5 - Labs (SQL Walkthrough) File

    • Lecture Audio/Video Recording (Access restricted to registered students): 

    • Lecture 5 - Labs Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

  • Tuesday, April 26, 2022; 9:15 AM - 10:15 AM

    Computer Laboratory A
    Narrow cohort and add measurements based on lab data, imaging metadata

    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

    • Submit lab 5, due Monday, May 2 at 5 pm Assignment
      Due: Monday, May 2, 2022, 5:00 PM
      Not available unless: You belong to Registered Students Only
    • Lab 5.html File
    • lab5.rmd File
    • lab 5 key File

  • Friday, April 29, 2022; 3:15 PM - 5:00 PM

    Computer Laboratory B
    Narrow cohort and add measurements based on lab data, imaging metadata

    Faculty:  Anobel Odisho

  • Tuesday, May 3, 2022; 8:45 AM - 9:15 AM

    Practical: PCORnet, Embedded RCTs
    Mark Pletcher: Using EHR data in randomized controlled trials. The PCORnet BP Control Laboratory and LHS Trials

    Faculty:  Mark Pletcher

    • Lecture Slides:

    • Lecture Audio/Video Recording (Access restricted to registered students): 

    • Lecture 6 Recording - Using EHR Data in RCTs Media Resource
      Not available unless: You belong to Registered Students Only
    • Lecture 6 Slides File

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Class recording 2021 Media Resource
      Not available unless: You belong to Registered Students Only
    • RCTs of EHR Interventions File
    • PCORnet BP Control Lab - Design Paper File
    • 2018 DCR Epi 202 Lecture Recording - Learning Healthcare System Research Projects (recorded live lecture) URL
      Not available unless: You belong to a group in Registered Students Only

  • Tuesday, May 3, 2022; 9:15 AM - 10:15 AM

    Computer Laboratory A
    Reshaping/Tidying Data.

    Faculty:   Anobel Odisho

    Location: Mission Hall MH-1400

  • Friday, May 6, 2022; 3:15 PM - 5:00 PM

    Computer Laboratory B
    Reshaping/Tidying Data

    Faculty:  Anobel Odisho

  • Tuesday, May 10, 2022; 8:45 AM - 9:15 AM

    Practical: Predictive analytics
    Sara Murray: The hazards of predictive analytics

    Faculty:  Sara Murray

    Location: Mission Hall MH-1400

    • Lecture Slides:

    • Lecture 7 Slides - Sara Murray File

    • Lecture Audio/Video Recording (Access restricted to registered students): 

    • Lecture 7 - Sara Murray Media Resource
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

  • Tuesday, May 10, 2022; 9:15 AM - 10:15 AM

    Computer Laboratory A
    Statistical Analysis of EHR data: univariate models Completion of student project with analytic output and interpretation

    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

    • Submit lab 7, due Monday, May 17 at 5 pm Assignment
      Due: Monday, May 17, 2021, 5:00 PM
      Not available unless: You belong to Registered Students Only
    • lab_7.html File

  • Friday, May 13, 2022; 3:15 PM - 5:00 PM

    Computer Laboratory B
    Statistical Analysis of EHR data: univariate models Completion of student project with analytic output and interpretation

    Faculty:  Anobel Odisho

  • Tuesday, May 17, 2022; 8:45 AM - 9:15 AM

    Practical: EHR Logs
    Julia Adler-Milstein: Using EHR Log data to study how clinicians use the EHR

    Faculty:  Julia Adler-Milstein

    Location: Mission Hall MH-1400

    • Lecture Slides:

    • Lecture Audio/Video Recording (Access restricted to registered students): 

    • Turning Digital "Fumes" into a Breath of Fresh Air Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Julia Adler Milstein - Lecture Discussion Media Resource
      Not available unless: You belong to Registered Students Only

    • Recommended Reading:

    • EHR Audit Logs: A Goldmine for Research File
    • EHR Audit Logs - Systematic Review File

  • Tuesday, May 17, 2022; 9:15 AM - 10:15 AM

    Computer Laboratory A
    Support for Final Project

    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

  • Friday, May 20, 2022; 3:15 PM - 5:00 PM

    Computer Laboratory B
    Support for Final Project

    Faculty:  Anobel Odisho

  • Tuesday, May 24, 2022; 8:45 AM - 9:15 AM

    Practical: TBD
    Leo Liu, TBD

    Faculty:  Leo Liu

    Location: Mission Hall MH-1400

    • Lecture Slides:

    • Lecture Audio/Video Recording (Access restricted to registered students): 

    • Leo Liu - Using ML to Predict Hospital Acquired Sepsis Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Recommended Reading:

    • Machine Learning and PICO File

  • Tuesday, May 24, 2022; 9:15 AM - 10:15 AM

    Computer Laboratory A
    Course faculty are available to address questions regarding the weekly assignment. Students may participate either in the larger forum or in smaller group discussions.

    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

  • Friday, May 27, 2022; 3:15 PM - 5:00 PM

    Computer Laboratory B
    Additional time for students to work on weekly assignments and ongoing projects with group-based and one-on-one assistance from course faculty.

    Faculty:  Anobel Odisho

  • Tuesday, May 31, 2022; 8:45 AM - 9:15 AM

    Practical: OMOP
    [proposed] Rohit Vashisht: New user design with propensity score matching using OMOP/UC-HDW

    Faculty: Rohit Vashisht

    Location: Mission Hall MH-1400

    • Lecture Slides:

    • Lecture Audio/Video Recording (Access restricted to registered students): 

    • Learning Effective Treatments for Chronic Disease from Real World Data _ Vashisht Media Resource

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

  • Tuesday, May 31, 2022; 9:15 AM - 10:15 AM

    Computer Laboratory A
    Support for Final Project

    Faculty:  Anobel Odisho

    Location: Mission Hall MH-1400

  • Friday, June 3, 2022; 3:15 PM - 5:00 PM

    Computer Laboratory B
    Support for Final Project.

    Faculty:  Anobel Odisho