UCSF Clinical Data

Many access paths, one point of entry

Need help or guidance? Do you need data with identifiers like birth dates or medical record numbers? Want to make sure you are compliant with regulations? Your first hour of consultation is free. Make sure you head in the right direction.

UCSF electronic health record data: What's available for research?

UCSF electronic health record (EHR) data:

  • APeX data dating back to 2012
  • STOR data dating back to 1988
  • Images
  • Clinical notes

Plus additional data, such as:

  • Geocoded address data
  • CA Death Registry data 
  • ZSFG and other Department of Public Health data
  • UC Health data (EHR data from UC Davis, UC Irvine, UCLA, UCSD, UCSF and many others) - patient counts available via ACT Network

>> COVID-19 specific data for research is also available

 

There’s a big difference between "identified" and "de-identified" data. And, a lot of acronyms!

Comparing de-identified data

Research Data Browser (RDB)

De-identified Clinical Data Warehouse

(De-ID CDW and De-ID OMOP)

Information Commons AWS Cluster
Learn more and access

Learn more and access

 

De-ID CDW Knowledge Base (login req'd)

Learn more and access

This is a subset of De-ID CDW Data in a custom data model

Will be replaced by De-ID CDW and decommissioned in the future

Additional data, including:
  • Financial data
  • Utilization data
  • Historical STOR data

Data based on De-ID CDW 

Plus:

  • Images**
  • Machine-redacted Clinical notes**
  • Concepts extracted from notes **
  Access via SQL server In cloud (AWS)
Useful for getting patient counts Suited for high speed queries & data mining
Large files, need analytics tool skills for queries  Berkeley Spark based, need SQL, Python or R skills

Includes De-identified Data from APex:

  • Demographics
  • Encounters
  • Diagnosis
  • Medications
  • Labs
  • Procedures
  • Flowsheets
  • Vital status from CA Death Registry
  • Refreshed monthly
Does not require IRB approval
Point & click interface available


** Requires IRB approval currently, but "certified" de-identified versions are coming.

First time User? Request access to Research Data and Tools 

Not sure what option is best for your project? Request a free brief consultation for advice.

Already using the De-identified clinical data warehouse or De-id OMOP? Join the active User Group! 

Request identified clinical data; you need a consultation

Identified data is provided by consultation only. The first hour of your consultation is free!

  • Clarity - closest data to APeX; clinical notes available
  • Clinical Data Warehouse (CDW) - concise, pulls common data in Clarity into one field
  • OMOP - uses a national common data model on data derived from PCORnet pSCANNER
    Data is further from original state and there is potential to lose information

The consultant will help you define a data specification. The APeX Pick List and/or ZSFG Pick List (Large Excel files via UCSF Box) are helpful tools for this work - see more information below.

Working with clinical data? Preparation is key.

Be ready with adequate computing capabilities and tools for:

Use the APeX Pick List  or the ZSFG Pick List (Large Excel files via UCSF Box) to identify variables for your research and to define your cohort.

  • Diagnoses
  • Meds
  • Labs
  • Procedures
  • Flowsheet
  • Departments
  • Smart Data Elements