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.
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.
|–||MSDW Custom Queries||Leaf||OMOP/ATLAS||TriNetX|
|Description||Work with MSDW analysts to compose custom SQL queries for research or QA. See our process.||Web-based, lightweight drag-and-drop query tool that quickly analyzes population demographics using ICD-10 codes.||A web-based integrated platform for database exploration, standardized vocabulary browsing, cohort definition, and population-level analysis.||A global research network that optimizes clinical research for data at Mount Sinai.|
|Access||Request form||Request access here. You can then use your Sinai network username/password to login.||Login to the ATLAS System using your Sinai School network username/password. For users with only a Hospital account, request a School account to access Atlas.||Request access here. Log in to the TriNetX system using your email address and password.|
|Training||Tutorial||Tutorial, Videos||PEAK Tutorial|
|Data Types||Conditions (diagnoses), procedures, demographics, encounters (patient encounter locations) and vitals||Facilities, diagnoses, procedures, medications, labs, orders, patient demographics||Demographics, diagnoses, procedures, medications, labs, vitals|
|PHI||Yes||No||Yes, if IRB Approved|
|Application Status||Leaf Status and Roadmap||ATLAS Status and Roadmap|
|Turnaround||Typically a few weeks (depending on complexity)||Seconds||Seconds||Seconds to minutes|
|Advantages/Disadvantages||Most comprehensive and sophisticated way to search the largest database at Mount Sinai||Can visualize demographic details of cohorts, drag-and-drop query feature||Utilizes common data model and queries; numerous query analysis tools available in github||Platform utilizes real-time modeling and simulation of patient populations based on inclusion and exclusion criteria; contains MSDW patient data through June 2021; can search BioMe patients; can search Image Research Warehouse patients; can be slow to operate|
Our custom query process in 7 easy steps. Please reach out to the MSDW group for more details on getting started.
|1.||Request Initiation & Review||A data request submitted through MSDW service desk (IRB requires protocol, approved IRB letter, and fund number to get started. QI projects require an approval letter written by a member of the QI board which details the requested data elements necessary for the project) is reviewed by a User Support Specialist who will follow up if there any questions or concerns regarding the request.|
|2.||Stakeholder Meeting||A User Support Specialist will schedule a date and time to meet and review the details of the data request; once confirmed, a meeting will be held through Zoom|
|3.||Project Analysis & Cost Estimate||The Clinical Infomaticist reviews notes from the meeting and determines the best approach for the necessary data. The Data Manager and an MSDW Analyst reviews the notes and the project request and delivers a cost estimate to complete the request. The P.I. from your research team must approve the estimate in order for development to begin.|
|4.||Development||Once the estimate is approved, the data request moves into the development queue and an MSDW Data Analyst will begin working on the request.|
|5.||Data Approval Meeting||A Data Analyst will schedule a date and time to review the dataset and confirm your satisfaction.|
|6.||Invoice for Fund Transfer||Once confirmed, MSDW will initiate a Fund Transfer using the fund number provided on the initial data request.|
|7.||Data Delivery||Upon completion of the Fund Transfer, the Data Manager delivers a link containing the confirmed dataset to all approved personnel.|
In compliance with HIPAA privacy and security, all data queries exclude the following protected patient categories:
- Special Status Patients: these patients include celebrities and public figures, Mount Sinai employees, providers, board members, donors, VIPs, and the family members of these patients.
- HIV-Related Patients: these patients include individuals who have HIV and/or AIDS; records include all lab tests for HIV irrespective of their outcome (positive or negative), and any records that are HIV-related, such as HIV screening, counseling, risk assessments, reasons for visits, past medical history, etc.
- Substance Use Patients: these patients include individuals who have received substance abuse disorder treatment at a federally funded facility (42 CFR Part 2) and individuals who have any data matching the substance use value sets as published by ResDAC.
- Community Connect Patients: these patients have seen Mount Sinai providers and also seen independent practices participating in the Mount Sinai Health Partners (MSHP) Clinically Integrated Network, but data from independent practices are excluded.
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 2).