UCSF COVID-19 Electronic Health Record Data For Research

Want access to electronic health record data on UCSF COVID-19 patients?

We are managing a UCSF COVID-19 Research Data Mart with IRB approval (IRB #20-30545, COVID-19 collaborative study for prospective and retrospective computational analysis). This will facilitate access for other researchers who would like access to these identified data for research.  If you do not require identified data, there are other options: 1) studies using "Limited Data" sets can qualify for Exempt review (see definition of "Limited Data") and 2) studies that can be done with completely de-identified data do not require IRB review under the 2018 Revised Common Rule. 

This UCSF COVID-19 Research Data Mart includes data extracts from the UCSF Electronic Health Record System (APeX) for patients who were tested for COVID-19 with either positive or negative results. The criteria for identifying COVID-19 patients is the same across UCSF for all reporting and is determined by the UCSF Medical Center.  This UCSF COVID-19 Research Data Mart includes:

  • Structured data (refreshed monthly)
  • Clinical notes (refreshed monthly)
  • Comparative/control data for patients not tested for COVID-19
  • With Information Commons tools available for data analyses

Get started!


Step 1. Submit a study proposal to the IRB

  • You must submit your own IRB for "Records Review."  IRB has established a COVID-19 Rapid Review Team and most reviews take under a week. Be sure to specify COVID-19 in study alias and reference IRB #20-30545, UCSF COVID-19 Research Data Mart in your IRB study.
    • As of April 27, 2020,  a new version of the IRB form has been released. If you have started your IRB application before April 27, 2020, please convert your application to the new form to answer the COVID-19-specific questions. Login to the wiki for more detailed instructions for completing the IRB application and notifying appropriate IRB personnel for review. 

Step 2. Once you have IRB approval, request data access

  • Follow the instructions on the UCSF wiki to request access. You will need to attach your approved IRB protocol application.
    • Depending on your study's requirements, you will either need to simply complete the terms of use for access to the UCSF COVID-19 Research Data Mart or meet with a consultant to assist you with your data needs. 


Need more information or more data? 


Login to access the UCSF COVID-19 Data Mart Wiki.  The wiki has FAQs, more details about the specifics of this Research Data Mart, instructions for IRB application submission, and many other support resources and links. It will be updated regularly.


ZSFG and San Francisco Data. Work is currently underway to create a dataset of COVID-19 patients from Zuckerberg San Francisco General Hospital (ZSFG). More information from San Francisco here


UC-Wide COVID Research Data Set (CORDS). UC Health EVP Carrie Byington requested UC BRAID, in coordination with the UC Health Data Warehouse (UCHDW) team, to accelerate the creation of a COVID Research Data Set (CORDS). The goal is to align our collective efforts to address the pandemic by creating a centralized, secure research data set and then facilitating access to this data set at the local level.  For more details on access and the data:  visit the Wiki  and see slides from the Research Data Series webinar. 


CA Dept Public Health (CDPH) Data. Through the UC Health-CDPH COVID Modeling Consortium, UC investigators have access to CDPH state-wide COVID data including labs, deaths, facilities, and locations. Data access is a simple 3-step process. Visit the consortium website to learn more about the datasets and how to access them.


National Data (N3C). The NIH/NCATS National COVID Cohort Collaborative (N3C) Data Enclave is a centralized, secure, national clinical data resource that the research community can use to study COVID-19, including potential risk factors, protective factors and long-term health consequences. Visit the NIH website to learn how to access N3C.


Note: Interested in Imaging Data? 


Utilizing Imaging Data for COVID-19 related research is being coordinated by Radiology and Biomedical Imaging. For collaborations using imaging, please send email to [email protected]