To provide the Mount Sinai Community with the very best data and resources to query the data, the Scientific Computing and Data team has been implementing improved infrastructure in the Mount Sinai Data Warehouse. In 2021, we debuted “MSDW2,” based on the OMOP Common Data Model, containing Epic data from throughout the Mount Sinai Health System, and unveiled two self-service query tools for defining and generating patient cohorts: Leaf and ATLAS.
Changes for Cohort Query Tool
While CQT has served our research community, CQT relies on infrastructure that is no longer updated with refreshed data. Researchers deserve access to updated, organized data, which is now available in MSDW2 through Leaf and ATLAS. This is why, effective December 20, 2021, the Cohort Query Tool will be decommissioned from use and will no longer be accessible.
What about my CQT work?
We understand that you may have saved cohorts or patient lists in CQT. With changes to the database and the query tools, there is no direct, easy way to transfer user data into a new tool application. We recommend the following options:
- Data Archive: Between now and December 20, run cohorts as patient lists. Once a patient list is generated, save the patient list as a local file to your computer. To continue using these patients in data queries, submit a custom data request through MSDW and work with one of our MSDW data analysts to continue your research. Click here to see more about MSDW custom queries.
- Leaf & ATLAS: Consider utilizing these query tools to generate cohorts or patient lists. A video training on how to use these tools has been recorded and added to the MSDW website. Click here for the recorded training, and click here for PowerPoint slides.
Final Notes
Monday, December 20, 2021 will be the final day Cohort Query Tool will be available. We ask that you save or transfer any work still in CQT before that date. Once CQT is decommissioned, saved cohorts will be deleted. We encourage all users to explore the new tools Leaf and ATLAS to query refreshed Epic patient data and, as always, to please submit a ticket with any questions or difficulties.