To allow researchers to explore the data in the Clinical Research Data Warehouse (CRDW) prior to making a data request, the CRI maintains two cohort discovery tools. Cohort discovery involves finding a patient population using different inclusion criteria, such as their age, medical conditions, and procedures they have undergone. Cohort discovery tools remove barriers between clinical data and end-users by making it easier to design and run self-service queries based on a cohort of interest. Cohort discovery tools can assist investigators in answering a variety of preparatory-to-research questions about a patient population such as: 1) assisting with determining if there are enough patients within the hospital system who have a given set of conditions matching the recruitment criteria for a trial, 2) helping plan or design a existing study or grant proposal.

The two applications the CRI currently maintains are: 1) BSD Leaf and 2) ITM Leaf

Leaf applications (“Leaf”) are powerful self-service tools which provides UChicago investigators a user-friendly interface for querying de-identified electronic health record (EHR) data sourced from the UChicago Medicine (UCM) patient population from single or multiple institutions. Leaf was created at the University of Washington’s Institute of Translational Health Sciences. More information about the background and creation of Leaf can be found in this JAMIA article.

What is BSD Leaf?

The BSD Leaf application allows for querying patient de-identified electronic health record data at the University of Chicago Medicine. The application provides counts and a basic demographic breakdown of the cohort and allows the end-user to review up to 500 rows of de-identified data. This information can be used as preparatory-to-research to see if there are enough patients that qualify for a study and to prepare an IRB protocol or grant proposal.

What data are in BSD Leaf?

BSD Leaf interacts directly with a regularly refreshed subset of data, derived from the EHR and encoded in the OMOP 6.0 data model. It encompasses patient interactions from 1/1/2012 – present and is updated weekly. Only a subset of OMOP 6.0 data concepts are available in the BSD Leaf application and currently includes Demographics, Diagnoses, Encounters, Labs, Medications, and Procedures.

BSD Leaf Eligibility:

BSD Leaf is available to all people at the University of Chicago with a CNET ID.

To Access BSD Leaf:

  1. BSD Leaf is behind the security firewall, so you will need to be on campus or using a VPN.
  2. Go to this website: https://bsdleaf.cri.uchicago.edu/
  3. Log-in with your CNET ID and password.
LOG IN TO BSD LEAF

 

BSD Leaf User Guide:

BSD LEAF USER GUIDE

What is ITM Leaf?

In partnership with the Institute for Translational Medicine (ITM), the CRI launched a federated clinical data query tool, ITM Leaf. The ITM, which is funded through the Clinical and Translational Science Awards (CTSA) Program from the National Institutes of Health National Center for Advancing Translational Sciences, is a partnership between the University of Chicago and RUSH in collaboration with Advocate Aurora Health, IIT, Loyola University Chicago, and NorthShore University HealthSystem. ITM institutions participating in the ITM Leaf initiative include the University of Chicago, RUSH, and Loyola.

The ITM Leaf application allows for federated querying across three institutions within the ITM: University of Chicago, RUSH, and Loyola. The data are from de-identified Electronic Health Records, and the application provides counts and a basic demographic breakdown of the cohort. This information can be used as preparatory-to-research to see if there are enough patients that qualify for a study and to prepare an IRB protocol or grant proposal.

What data are in ITM Leaf?

ITM Leaf interacts directly with a regularly refreshed subset of de-identified EHR data that is encoded in the PCORnet 6.0 data model. It encompasses patient interactions from 1/1/2017 to 12/31/2022 and is updated quarterly. Only a subset of PCORnet 6.0 data concepts are available in the ITM Leaf application. Information on the data available in the tool can be found here. Documentation will be updated as new concepts are available. Please note that our partner institution, Loyola, maintains the data specification documents for ITM Leaf.

ITM Leaf Eligibility:

ITM Leaf is available to all people at the University of Chicago who are eligible to be on an IRB approved study. This means that users must have current University of Chicago BSD CITI training and HIPAA information security training. Users do not need an approved IRB protocol to access ITM Leaf.

To Access ITM Leaf:

  1. ITM Leaf is behind the security firewall, so you will need to be on campus or using a VPN.
  2. Go to this website: https://itmleaf.cri.uchicago.edu/
  3. Log-in with your CNET ID and password.

ITM Leaf Training Videos:

ITM Leaf Training Videos are available to help you get started, show examples of how to perform queries of different complexities, and troubleshoot your queries.

You can click on the following video links to open them in a new tab. These videos were created by our partner institution, Loyola. You will need to follow the access instructions above to navigate to the UChicago ITM Leaf application.

For more information, please visit: https://chicagoitm.org/itm-leaf/

Q: What are the uses of Leaf?

A: Leaf can assist researchers in creating new research hypotheses, identifying potential cohorts for clinical trials, and reducing the time spent on study feasibility and subject recruitment. It is also a way for potential CRDW users to become familiar with the data elements we have available.

Q: When should I use BSD Leaf vs. ITM Leaf?

A: Choosing which Leaf application is right for you depends on your research question and your desire to federate and look beyond University of Chicago Medicine for your cohort of interest. Please review the specifications for each Leaf application to determine which is right for you.

Q: What credentials do I need to access BSD Leaf and ITM Leaf?

A: You can access the BSD and ITM Leaf applications with your CNET credentials. You must be on a secure University network to access either Leaf application. If you are working off campus, please log into the University’s VPN. Please note that ITM Leaf authenticates against valid CITI and HIPAA training in addition to an active CNET account.

Q: Can I export de-identified data from BSD or ITM Leaf?

A: The interface does not currently support direct exporting of de-identified data. If your cohort discovery results are promising and you would like a full data extract, please follow the process for placing a CRDW data request.

Q: How can I get technical help with BSD or ITM Leaf?

A: If assistance is needed, please contact cri-app-dev@lists.uchicago.edu and indicate the application you are requesting assistance with in the subject line. You should expect a reply within 24-48 hours.