Mount Sinai Data Warehouse
Partnering with researchers and clinicians to effectively utilize Mount Sinai Health System data for translational and clinical research
Announcements
2025 – AIR·MS (Artificial Intelligence-Ready Mount Sinai) is a cloud-based, multi-modal health data platform that integrates patient data generated from different clinical departments across Health Systems. At this time, the following datasets are offered on the platform:
- Identifiable and de-identified versions of Mount Sinai Data Warehouse (MSDW) datasets.
- Clinical notes in the form of unstructured data (progress notes, telephone encounters, nursing notes, procedures, etc.) that have been enabled with in-memory full-text search capabilities empowering researchers to build patient cohorts based on terms contained in unstructured reports in seconds or even milliseconds!
- Pathology metadata which will aid researchers in the field of Computational Pathology.
October 2024-March 2025 – Scientific Computing and Data, Mount Sinai Innovation Partners, the Department of Molecular Pathology, and Tisch Cancer Institute have partnered with genomic testing vendors to develop a genomic research data warehouse comprised of somatic genomic testing results ordered at all Mount Sinai facilities. All somatic genomic tests performed by Foundation Medicine and Caris for Mount Sinai patients are hosted on MSDW in multiple data formats, encompassing both structured and raw genomic data. For more information click here.
October, 2024 – Scientific Computing and Data is pleased to announce that all current and historic patient home addresses recorded in Epic have been geocoded using the Decentralized Geomarker Assessment for Multi-Site Studies (DeGAUSS) application and are now stored in the Mount Sinai Data Warehouse (MSDW). Access to this new data source at the patient-level will only be available to researchers, who have a relevant IRB approved protocol, via a MSDW custom data request. If you have any questions about accessing these new data sources, please contact the MSDW team (MSDW support).
May, 2024 – As of May 9, 2024, the MSDW chargeback rate is $236 per hour. For any questions, please reach out to ranjini.kottaiyan@mssm.edu.
OMOP Query Tools
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.
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.
TriNetX
A web-based query tool that queries de-identified Epic data, including demographics, diagnoses, lab results and more. Request Access.
Data Sets
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.
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.
OMOP Data Marts
MSDW supports continually refreshed OMOP-formatted data marts of your research projects’ patient cohorts of interest.
Services
CTSA CD2H
CTSA National Center for Data to Health (CD2H) provides additional resources to the community.
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.