{"id":44,"date":"2020-02-05T14:28:06","date_gmt":"2020-02-05T14:28:06","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/msdw\/?page_id=44"},"modified":"2026-09-17T05:33:13","modified_gmt":"2026-09-17T09:33:13","slug":"services","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/msdw\/services\/","title":{"rendered":"Services"},"content":{"rendered":"

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Scientific Computing and Data<\/a>\u00a0\/\u00a0Mount Sinai Data Warehouse<\/a> \/ Services<\/p>\n

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MSDW Services<\/h1>\n

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<\/a> for OMOP CDM. Custom data requests (which can include PHI) may be requested through the MSDW Data Request Form<\/a>. To initiate the custom data request process, please submit a request through the MSDW ticketing system<\/a>.<\/p>\n

All data queries and tools are designed to meet the requirements of federal HIPAA law with Protected Patient Exclusion Criteria<\/a>.<\/p>\n

MSDW Data<\/h2>\n

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<\/p>\n\n\n\n\n\n\n\n\n\n\n
–<\/span><\/td>\nMSDW Custom Data Set<\/strong><\/span><\/td>\nCOVID-19 Research Data<\/strong><\/span><\/td>\nData Marts<\/strong><\/span><\/td>\n<\/tr>\n
Description<\/strong><\/td>\nWork with MSDW analysts to compose custom SQL queries for research or QA.\u00a0 See our process.<\/a><\/td>\nThe<\/span>\u00a0<\/span>de-identified COVID-19 data sets\u00a0<\/span>include all patients at a Mount Sinai facility who have been\u00a0<\/span>screened for or\u00a0<\/span>diagnosed with\u00a0<\/span>COVID<\/span>-19<\/span>. The identified version of this data set is available with\u00a0<\/span>appropriate documents. Data is refreshed weekly. See more details<\/a>.<\/span><\/td>\nAn 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).<\/td>\n<\/tr>\n
Data Types<\/strong><\/td>\nPatient 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<\/a>\u00a0for more information on MSDW data.<\/td>\nPatient Encounters (Demographics, Comorbidities, Outcomes), Vital Signs, Labs, Medication Administrations, and Radiology Report Impressions. COVID-19 vaccine immunization file added in February 2021<\/td>\n\u00a0<\/td>\n<\/tr>\n
Access<\/strong><\/td>\nRequest Custom Data Set form<\/a><\/td>\nDownload De-Identified Data<\/a><\/td>\nNavigate to the\u00a0MSDW Service Desk<\/a>\u00a0and submit a ticket for \u201cAsk a Question.\u201d Ticket must include an attached signed\u00a0MSDW Database Access Agreement<\/a>\u00a0and IRB documentation (if applicable).<\/td>\n<\/tr>\n
Cost<\/strong><\/td>\n$177\/hour<\/td>\nDe-identified data is available to Mount Sinai Researchers. Researchers seeking a custom COVID-19 data set, requests are subject to a fee of $177\/hour. Submit a request for custom data here<\/a>.<\/td>\n$177\/hour<\/td>\n<\/tr>\n
PHI<\/strong><\/td>\nYes<\/td>\nYes<\/td>\nYes<\/td>\n<\/tr>\n
Turnaround Time<\/strong><\/td>\nTypically a few weeks (depending on complexity)<\/td>\nDownload in seconds<\/td>\nOne to a few days (depending on complexity)<\/td>\n<\/tr>\n
Advantages<\/strong><\/td>\nMost comprehensive and sophisticated way to search the largest database at Mount Sinai<\/td>\nMount Sinai COVID-19 data sets are refreshed weekly<\/td>\nHigh-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<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

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Cohort Query Tools<\/h2>\n

Self-service query tools can be utilized to query de-identified MSDW data directly. For additional information on the data services offered, Digital Concierge<\/a> hours are hosted weekly. Compare Leaf and ATLAS tools directly<\/a> in their similarities, inclusion criteria, and capabilities.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n
–<\/span><\/td>\nLeaf<\/strong><\/span><\/td>\nATLAS<\/strong><\/span><\/td>\nTriNetX<\/strong><\/span><\/td>\n<\/tr>\n
Description<\/strong><\/td>\nWeb-based,\u00a0lightweight drag-and-drop cohort query tool that quickly analyzes population demographics<\/td>\nA web-based cohort query tool for database exploration, standardized vocabulary browsing, cohort definition, and patient cohort-level analysis<\/td>\nA web-based cohort query tool<\/td>\n<\/tr>\n
Access<\/strong><\/td>\nUse your Mount Sinai network username\/password to login.<\/td>\nUse your Mount Sinai network username\/password to login<\/td>\nRequest access here<\/a>. Log in to the TriNetX system<\/a> using your email address and password.<\/td>\n<\/tr>\n
Training<\/strong><\/td>\nWritten Tutorial<\/a>; PEAK Tutorial<\/a><\/td>\nWritten Tutorial<\/a>; PEAK Tutorial<\/a>; Videos<\/a><\/td>\nPEAK Tutorial<\/a><\/td>\n<\/tr>\n
Data Types<\/strong><\/td>\nPatient demographics, diagnoses, procedures, medications, labs, orders, vitals, institutional patient cohorts (BioMe, IRW, etc.)<\/td>\nPatient demographics, diagnoses, procedures, medications, labs, orders, vitals<\/td>\nPatient demographics, diagnoses, procedures, medications, labs, orders, vitals<\/td>\n<\/tr>\n
PHI<\/strong><\/td>\nNo<\/td>\nYes, if IRB Approved<\/td>\nDe-identified data only<\/td>\n<\/tr>\n
Cost<\/strong><\/td>\nNo charge<\/td>\nNo charge<\/td>\nNo charge<\/td>\n<\/tr>\n
Application Status<\/strong><\/td>\nLeaf Status and Roadmap<\/a><\/td>\nATLAS Status and Roadmap<\/a><\/td>\n\u00a0<\/td>\n<\/tr>\n
Advantages<\/strong><\/td>\nCan visualize demographic details of cohorts, drag-and-drop query feature; download de-identified patient cohort list<\/td>\nUtilizes common data model and queries<\/td>\nOffers a polished, commercially developed user interface<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Protected Patient Information<\/span><\/h2>\n

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<\/a> for more information about Protected Patient Categories.<\/p>\n

We are supported by grant UL1TR004419 from the National Center for Advancing Translational Sciences, National Institutes of Health.<\/p>\n

\u00a0<\/p>\n

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Scientific Computing and Data\u00a0\/\u00a0Mount Sinai Data Warehouse \/ Services MSDW ServicesMSDW 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 […]<\/p>\n","protected":false},"author":600,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"
\"\"<\/td>Please submit a request at the\u00a0MSDW ticketing system<\/a>\u00a0and one of our specialists will reach out to you.\u00a0 For more information into the research process please click here<\/a> to learn about the Digital Concierge services available.<\/td><\/tr><\/tbody><\/table>

\u00a0<\/p>
Core Services<\/strong><\/td><\/tr>
MSDW has data throughout the system since 2003, covering 3.5 million patients, 25 million visits, and billions of facts. As data is passed from individual systems into the MSDW, it is validated and re-organized. Not all data from each system is passed to the MSDW, though requests can be made. A complete list of sources<\/a> and a data dictionary<\/a> is available and frequently refined.<\/td><\/tr><\/tbody><\/table>
-<\/span><\/td>Custom Queries<\/strong><\/span><\/td>Cohort Query Tool<\/strong><\/span><\/td>i2b2<\/strong><\/span><\/td>OMOP\/ATLAS<\/strong><\/span><\/td><\/tr>
Description<\/strong><\/td>Work with MSDW analysts to compose custom SQL queries for research or QA.\u00a0 See our 10-Step process.<\/a><\/td>Web-based way to browse aggregated, de-identified (or identified, if IRB-approved) data from Epic, Cerner, Eagle, TDS and other systems in the MSDW.<\/td>Web-based way to browse aggregated, de-identified data from Epic, Cerner, Eagle, TDS and other systems in the MSDW.<\/td>A web-based integrated platform for database exploration, standardized vocabulary browsing, cohort definition, and population-level analysis.<\/td><\/tr>
Access<\/strong><\/td>Request form<\/a><\/td>Request access\u00a0here<\/a>.\u00a0 You can then use your Sinai network username\/password to login.<\/td>Request access\u00a0here<\/a>.\u00a0You can then use your Sinai network username\/password to login.<\/td>Login to the\u00a0Atlas System<\/a>\u00a0using your Sinai network username\/password.<\/td><\/tr>
Training<\/strong><\/td>\u00a0<\/td>Tutorial<\/a><\/td>Tutorial<\/a><\/td>Tutorial<\/a><\/td><\/tr>
Data Types<\/strong><\/td>\u00a0<\/td>Facilities, Diagnoses & DRGs, Procedures, Meds, Labs, Orders, EKG reports, Rads reports, Path reports, Histories and Clinical Documentation, Patient demographics.<\/td>Providers, Diagnoses, Procedures, Meds, Labs, Documentation, Patient demographics.<\/td>\u00a0<\/td><\/tr>
PHI<\/strong><\/td>Yes<\/td>Yes, if IRB approved<\/td>No<\/td>\u00a0<\/td><\/tr>
Cost<\/strong><\/td>$180\/hr<\/td>De-identified data covered by Mount Sinai Re-identification of data is $160\/hr<\/td>Free<\/td>Free<\/td><\/tr>
Turnaround<\/strong><\/td>Typically a few weeks (depending on complexity)<\/td>Seconds<\/td>Minutes<\/td>Seconds<\/td><\/tr>
Advantages\/Disadvantages<\/strong><\/td>Most comprehensive and sophisticated way to search the largest database at Mount Sinai<\/td>characterize cohorts in MSDW. Can visualize demographic details of cohorts, Top 10 lists.
Patients with any HIV history (even PEP) suppressed from results<\/td>		Robust, approximate method to cohorts in MSDW; permits more sophisticated queries than CQT, and can plot results over time.
Can share queries with colleagues, and build cohorts for future analysis.<\/td>		\u00a0<\/td><\/tr>
Typical Queries<\/strong><\/td>Tabulate demographics, comorbidities, PMD and SW\/Care Management involvement in geriatric patients discharged from the ED who were re-admitted within 3, 6 or 12 months<\/td>How many patients over age 70 received appendectomy at MSH in 2016?<\/td>

How many patients with a diagnosis of Lyme disease received multiple rounds of doxycycline?<\/p>

How many patients with a troponin <=1 got cardiac catheterization, and when?<\/p><\/td>

\u00a0<\/td><\/tr><\/tbody><\/table>

\u00a0<\/p>

<\/a>Custom Query Intake Process<\/span><\/h2>

Our custom query process in 10 easy steps.\u00a0 Please reach out to the MSDW group<\/a> for more details on getting started<\/p>

\u00a0<\/p>

\"\"<\/p>

\u00a0<\/p>

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