Scientific Computing and Data / Mount Sinai Data Warehouse / Services
MSDW Services
MSDW has Epic Electronic Health Record data from the Mount Sinai Health System, which includes demographics, encounters, labs, conditions, diagnoses, medications and more. Data is transformed from Epic into OMOP CDM and is updated daily. Reference OHDSI’s data dictionary for OMOP CDM. Custom data requests (which can include PHI) may be requested through the MSDW Data Request Form. To initiate the custom data request process, please submit a request through the MSDW ticketing system.
All data queries and tools are designed to meet the requirements of federal HIPAA law with Protected Patient Exclusion Criteria.
MSDW Data
The Mount Sinai Data Warehouse provides researchers access to data on the over 12 million unique patients in the Mount Sinai Health System Epic Electronic Health Record (EHR). Data containing PHI is accessible through approved IRB documentation
| – | MSDW Custom Data Set | COVID-19 Research Data | Data Marts |
| Description | Work with MSDW analysts to compose custom SQL queries for research or QA. See our process. | The de-identified COVID-19 data sets include all patients at a Mount Sinai facility who have been screened for or diagnosed with COVID-19. The identified version of this data set is available with appropriate documents. Data is refreshed weekly. See more details. | An MSDW Data Mart is a curated, customized data set with a specific focus. There are two categories of Data Marts: Analyst-generated curated data marts (e.g. Liver data), and User-requested data marts (i.e. your custom MSDW data request). |
| Data Types | Patient Records with Encounters, Clinical Data, Diagnoses (ICD-9 and ICD-10), Medication Records (prescription and medication administrations), Test Results (including radiology and pathology), Clinical Documentations (including operative reports, discharge summaries). Click here for more information on MSDW data. | Patient Encounters (Demographics, Comorbidities, Outcomes), Vital Signs, Labs, Medication Administrations, and Radiology Report Impressions. COVID-19 vaccine immunization file added in February 2021 | |
| Access | Request Custom Data Set form | Download De-Identified Data | Navigate to the MSDW Service Desk and submit a ticket for “Ask a Question.” Ticket must include an attached signed MSDW Database Access Agreement and IRB documentation (if applicable). |
| Cost | $180/hour | De-identified data is available to Mount Sinai Researchers. Researchers seeking a custom COVID-19 data set, requests are subject to a fee of $180/hour. Submit a request for custom data here. | $180/hour |
| PHI | Yes | Yes | Yes |
| Turnaround Time | Typically a few weeks (depending on complexity) | Download in seconds | One to a few days (depending on complexity) |
| Advantages | Most comprehensive and sophisticated way to search the largest database at Mount Sinai | Mount Sinai COVID-19 data sets are refreshed weekly | High-quality research data is curated by our Clinical Informaticists; data quality is maximized by professional processing and repeat use; expanded opportunities for collaboration and citations |
Cohort Query Tools
Self-service query tools can be utilized to query de-identified MSDW data directly. For additional information on the data services offered, Digital Concierge hours are hosted weekly. Compare Leaf and ATLAS tools directly in their similarities, inclusion criteria, and capabilities.
| – | Leaf | ATLAS | TriNetX |
| Description | Web-based, lightweight drag-and-drop cohort query tool that quickly analyzes population demographics | A web-based cohort query tool for database exploration, standardized vocabulary browsing, cohort definition, and patient cohort-level analysis | A web-based cohort query tool |
| Access | Use your Mount Sinai network username/password to login. | Use your Mount Sinai network username/password to login | Request access here. Log in to the TriNetX system using your email address and password. |
| Training | Written Tutorial; PEAK Tutorial | Written Tutorial; PEAK Tutorial; Videos | PEAK Tutorial |
| Data Types |
Patient demographics, diagnoses, procedures, medications, labs, orders, vitals, institutional patient cohorts (BioMe, IRW, etc.) |
Patient demographics, diagnoses, procedures, medications, labs, orders, vitals |
Patient demographics, diagnoses, procedures, medications, labs, orders, vitals |
| PHI | No | Yes, if IRB Approved | De-identified data only |
| Cost | No charge | No charge | No charge |
| Application Status | Leaf Status and Roadmap | ATLAS Status and Roadmap | |
| Advantages | Can visualize demographic details of cohorts, drag-and-drop query feature; download de-identified patient cohort list | Utilizes common data model and queries | Offers a polished, commercially developed user interface |
Protected Patient Information
In compliance with HIPAA privacy and security, all data queries exclude protected patient categories. These records are excluded from de-identified OMOP data sets and from PHI data sets unless explicitly approved by the investigator’s IRB (42 CFR Part 46). Click here for more information about Protected Patient Categories.
We are supported by grant UL1TR004419 from the National Center for Advancing Translational Sciences, National Institutes of Health.