Mount Sinai Data Warehouse

Partnering with researchers and clinicians to effectively utilize Mount Sinai Health System data for translational and clinical research


July 13, 2023  We are pleased to announce two new features added to the Leaf cohort query tool: a new Timelines feature and an improved lab results concept category. A guide for using Timelines is available here. The concept category currently named Lab Results (LOINC) has been updated to: Lab Results and Measurements, and concepts that do not have any measurements associated with them or any of their descendants have been removed. Users can now define specific values or ranges (i.e. equal to, greater than, less than, etc) for lab results or measurements in their query.

March 8, 2023 Computational and data science ecosystem is available for Oncology researchers to gain insights to further their research. There are HP resources, EHR cohort query tools, data resources and electronic data capture systems available here. Expertise is available to support researchers with tools, data access, and consultations.

February 23, 2023 Thank you to those who attended the introductory training session for Leaf and ATLAS cohort query tools today! Please see the PowerPoint Slide Deck and the session’s Video Recording. You can review all previous session materials on our Training and Tutorials page.

January 5, 2023 – Save the date: Mount Sinai Data Warehouse’s Town Hall will be Tuesday, May 2, at 11:00 AM. Registration and details coming soon.

December 28, 2022 – Interactive training courses for Leaf and ATLAS are now available in PEAK! “Leaf Application Training: Introduction” provides an overview of Leaf access and functions, and “ATLAS Query Application Introduction Training” navigates step-by-step instructions for beginner ATLAS users.

OMOP Query Tools

Which tool should I use?


A web-based query tool that creates patient cohorts from de-identified data using clinical and demographic criteria. Log in with your Mount Sinai credentials.

Resources and Info  |  Launch Leaf 


A web-based query tool that analyzes data standardized in the OMOP CDM format. Mount Sinai users must have a school account for access.

Resources and Info  |  Launch ATLAS


A web-based query tool that queries de-identified Epic data, including demographics, diagnoses, lab results and moreRequest Access.

TriNetX Tutorial  |  Launch TriNetX

COVID-19 Data Sets

The de-identified COVID-19 data sets include all patients at a Mount Sinai facility who have been screened for or diagnosed with COVID

Resources and Info | Download Data

Custom Data Request

The MSDW team will work with you to create a custom de-identified or PHI data set for your research or quality improvement project. 

Resources and Info | Data Set Request Form

OMOP Data Marts

MSDW supports continually refreshed OMOP-formatted data marts of your research projects’ patient cohorts of interest.

Resources and Info | Request Access


CTSA National Center for Data to Health (CD2H) provides additional resources to the community.

CTSA Resources | Conduits 

Enterprise Data Catalog

Enterprise Data Catalog (EDC) at Mount Sinai features a collaborative environment to share data and information.

Launch EDC

Tools for OMOP

Open source software tools can be used with MSDW’s Observational Medical Outcomes Partnership (OMOP) Common Data Model.


Acknowledge Mount Sinai in Your Work

All publications must include the following language in the acknowledgments section: “This work was supported in part through the Mount Sinai Data Warehouse (MSDW) resources and staff expertise provided by Scientific Computing and Data at the Icahn School of Medicine at Mount Sinai.” 

Supported by grant UL1TR004419 from the National Center for Advancing Translational Sciences, National Institutes of Health.