Cohort Selection Tool FAQs

What is the Cohort Selection Tool (CST)?

The CST is a tool that you use to query UCSF’s clinical data from the Integrated Data Repository (IDR). The IDR currently contains a de-identified copy of the UCSF Medical Center APeX database and the UCSF School of Dentistry Dental Clinic database (Axium). 

Using this tool to explore the patient populations contained in these data sources, you can test the feasibility of recruiting cohorts to test particular hypotheses.

The CST is available at or through your MyResearch account.

Do I need a separate username and password to access the CST?

No. You use your Campus AD username and password to sign in directly to the CST. It can also be accessed through your MyResearch account.

What data is available in the CST?

The CST currently accesses a de-identified portion of the UCSF Medical Center APeX database and the UCSF School of Dentistry Dental Clinic database (Axium).

How can I use the counts I find in the CST?

CST counts can be used for cohort planning, correlation analysis, risk analysis, etc.

What is Epic?

Epic offers an integrated suite of health care software that supports functions related to patient care, including registration and scheduling; clinical systems for doctors, nurses, emergency personnel, and other care providers; systems for lab technicians, pharmacists, and radiologists; and billing systems for insurers.

 At UCSF, we have re-branded our Epic HER system as APeX.

What is i2b2?

i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center has developed a scalable informatics framework that enables clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origins.  i2b2 is funded as a cooperative agreement with the National Institutes of Health.

UCSF uses the i2b2 tools to support the IDR, UC ReX and other projects.

How do I create a query?

To create a query, complete the appropriate Query Tool columns using information from the Navigate Terms and Find Terms tabs located on the upper left-hand side of the CST screen.

How do I save a query?

Queries that you create are automatically saved for you after you run them. Your queries are listed in the Previous Queries section located on the lower left-hand side of the CST screen.

How do I add more groupings/categories?

To add additional Groups, click the New Groups button at the bottom on the bottom right-hand side of the CST screen.

How can I rerun a saved query?

Your queries are saved in the Previous Queries section located in the lower left-hand side of the CST screen. To re-run a previous query, select and drag the appropriate query into the Query Name field on the Query Toll tab in the upper right-hand side of the CST screen. You can modify the previously entered search criteria that you entered in the Groups column.

How do I get access to identified data after I have used the CST?

If you have identified a potential cohort for your study utilizing the Cohort Selection Tool, the Academic Research Systems (ARS) team can extract the corresponding identifiers for your patient population with proper CHR protocol approval.

This extract will be delivered to you in your MyResearch account to ensure the continued security of the data.  

These services are available to all researchers at UCSF and affiliated institutions and can be requested through your MyResearch account by clicking the Clinical Data Research Consultations Request Form icon. 

How accurate are the cohort patient counts?

Counts are + or – 3 counts. The uncertainty in the counts is introduced to ensure that data is not re-identifiable.

How up-to-date or frequently is the data being refreshed?

Data is refreshed every other week.

Where do I go for additional support and/or answers to CST related questions?