Use of Electronic Health Record Data for Research

Spring 2024 (3 units)

Electronic Health Record (EHR) data can be used for a variety of clinical, epidemiologic and translational research, and these data are becoming more accessible. This course introduces students to concepts, methods, and pitfalls related to the extraction, manipulation and analysis of data from EHRs. The course covers common EHR data structures and vocabularies, using that knowledge to inform research study design, and creation of patient cohorts and analytic extracts. We will cover both ambulatory and inpatient use cases. Students have the opportunity to design their own research projects during the course.


Each week, new material is introduced via a recorded lecture and recommended readings. After beginning to study the lecture and reading on their own, the class gathers for a Large Group Discussion in which the lecture is briefly reviewed and students have the opportunity to pose questions to course faculty or prompt discussion on any aspect of the material. A Computer Laboratory session immediately follows, providing students with time to work on their problem sets with supervision and assistance from course leaders. A second Computer Laboratory occurs at the end of the weekly cycle, allowing students to finish their assignments, resolve outstanding questions, and receive advice about their own ongoing projects.

Large Group Discussion:
Brief review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.
Time: Tuesdays, 9:00 to 9:30 AM, beginning April 2

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.
Time: Tuesdays, 9:30 to 10:10 AM, beginning April 2

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.
Time: Fridays, 3:15 to 5:00 PM, beginning April 5

The weekly learning cycle, therefore,

a) begins on a Monday when the recorded lecture, detailing the weekly content, is released on video;
b) has curricular emphases noted and clarifications provided on Tuesday with a large group discussion and class time to begin work on the weekly assignment;
c) reinforces learning for the next several days as students continue to work on the assignment and their individual project via self-study and group study;
d) has additional faculty availability on Friday for questions and discussion; and
e) ends on the following Monday with the submission of the completed weekly assignment.



Prior to the beginning of the course, students should obtain access to the UCSF Research Analysis Environment (RAE), the UCSF de-identified Clinical Data Warehouse, and the UCSF Git (a system that allows you to share and collaborate on source code). Please begin the process of obtaining access at least 1 week prior to the course.

RAE also contains instances of R and Stata to manipulate and analyze data obtained from the de-identified EHR warehouse, but students may wish to use their own copies of this software outside of RAE.

All course materials and handouts will be posted on the course's online syllabus.


Grades will be based on total points achieved on the weekly problem set homework assignments (~70%) and the final project (~30%). Late assignments are not accepted. Answer keys to problem sets will be posted shortly after the turn-in deadline.

Students not in full-year TICR Programs who satisfactorily pass all course requirements will, upon request, receive a Certificate of Course Completion.

Only UCSF students (defined as individuals enrolled in UCSF degree or certificate programs) will receive academic credit for courses. Official transcripts are available to UCSF students only. A Certificate of Course Completion will be available upon request to individuals who are not UCSF students and satisfactorily pass all course requirements.

UCSF Graduate Division Policy on Disabilities

To Enroll

ATCR and MAS students use the Student Portal

Students taking individual courses:

Course Fees
How to pay (please read before applying)
Only one application needs to be completed for all courses desired during the quarter.

Spring 2023 Course Schedule. Spring 2024 schedule available Feb 1.

Apply for Srping courses by March 1, 2024.  Spring 2024 application available Feb 1.