Mount Sinai Data Warehouse

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

 Announcements

PREVIOUS ANNOUNCEMENTS:

February, 2024 –  Leaf and ATLAS cohort query tools will be unavailable Wednesday, February 7, 2024, 5 pm – 9 pm. We are updating the tools to apply recommended system and security patches. If you have questions, please contact Leaf and ATLAS support.

Announcing January 2024 Training:

Introduction to TriNetX – Wednesday, January 10, 12 pm – 1 pm
Introduction to Leaf & ATLAS – Wednesday, January 17, 12 pm – 1 pm
[See this page to access slides and presentation videos]

December 4, 2023  The Mount Sinai Data Warehouse (MSDW) and the Biomedical Engineering and Imaging Institute (BMEII) teams are pleased to announce the addition of the Mount Sinai Imaging Research Warehouse (IRW) 2.0 cohort to the Leaf cohort query tool and MSDW. The IRW 2.0 cohort consists of over 1.5 million patients who have at least one imaging study available in the new Imaging Research Warehouse. The Leaf cohort query tool allows users to identify patients in the IRW 2.0 cohort meeting specific clinical and demographic inclusion and exclusion criteria.
Please see the tutorials on Leaf available on this website. You can also request support for Leaf or MSDW using the links shown hereAdditional information on the Imaging Research Warehouse 2.0 can be found on the Biomedical Engineering and Imaging Institute (BMEII) website.

Training: Leveraging Epic for Research – Tuesday, November 7, 2023 12 pm – 1 pm (now ZOOM ONLY)

On behalf of Dean Patricia Kovatch, we invite you to join the whole Scientific Computing and Data team for an in-person Open House, Monday October 23, 12-1 pm, Goldwurm Auditorium at the Icahn Medical Institute (1st Floor). Coffee, tea, cookies and cake will be provided.

The MSDW Town Hall will be held Tuesday, October 24, 2 pm – 3 pm. This will be a hybrid session located in Hess Center for Science & Medicine (CSM) Seminar Room A (2nd Floor) and on Zoom webinar.

October 2023 Training:

– Introduction to Leaf & ATLAS – Wednesday, October 11, 12 pm – 1 pm
– Introduction to TriNetX – Wednesday, October 18, 12 pm – 1 pm

October 19, 2023  We are pleased to announce greatly improved standard healthcare codes in the Mount Sinai Data Warehouse (MSDW) OMOP database that enable building patient cohorts in the Leaf, ATLAS, and TriNetX cohort query tools. These standard codes now cover 98% of the data, and with higher quality, for diagnoses, lab results, medications and immunizations, procedures and surgical procedures, and allergies. OMOP refers to the Observational Medical Outcomes Partnership Common Data Model open community data standard used by MSDW.

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.

 

OMOP Query Tools

Which tool should I use?

Leaf

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 

ATLAS

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

TriNetX

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 CD2H

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.

OMOP CDM ToolsOHDSI.org

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.