{"id":42,"date":"2020-02-05T14:26:58","date_gmt":"2020-02-05T14:26:58","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/msdw\/?page_id=42"},"modified":"2025-06-09T11:47:13","modified_gmt":"2025-06-09T15:47:13","slug":"faqs","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/msdw\/faqs\/","title":{"rendered":"FAQs"},"content":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.22″][et_pb_row _builder_version=”3.25″ background_size=”initial” background_position=”top_left” background_repeat=”repeat”][et_pb_column type=”4_4″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_text admin_label=”Breadcrumb” _builder_version=”4.9.0″ _module_preset=”default”]Scientific Computing and Data<\/a>\u00a0\/\u00a0Mount Sinai Data Warehouse<\/a> \/ Frequently Asked Questions
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<\/a>Frequently Asked Questions<\/h1>\n

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General<\/span><\/h2>\n

Q: How can I identify eligible cohorts available in MSDW?<\/a><\/span><\/p>\n

Q: What Data sources are available in the Data Warehouse?<\/a><\/span><\/p>\n

Q: How far back does the data go?<\/a><\/span><\/p>\n

Q: How often is the data refreshed?<\/a><\/span><\/p>\n

Q: What data is available in MSDW?<\/a><\/span><\/p>\n

Q: Does MSDW and de-identified and PHI data?<\/a><\/span><\/p>\n

Q: What information is available in the Enterprise Data Catalog?<\/a><\/span><\/p>\n

Q: Is there a centralized information point regarding all data available to Sinai researchers?<\/a><\/span><\/p>\n

Q: If I want identifiable data or a custom report, what should I do?<\/a><\/span><\/p>\n

Q: How much are the Data Warehouse services?<\/a><\/span><\/p>\n

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Cohort Query Tools<\/span><\/h2>\n

Q: Which Cohort Query Tool should I use?<\/a><\/span><\/p>\n

Q: How do you compare Leaf, ATLAS, and TriNetX from a user perspective?<\/a><\/span><\/p>\n

Q: I am getting an error when trying to access or log in to Leaf or ATLAS. What do I do?<\/a><\/span><\/p>\n

Q: Do I need to request access every time I want to use a query tool to review de-identified data?<\/a><\/span><\/p>\n

Q: Is it possible to get number of patients for a particular disease that are not getting treatment (i.e. new diagnosis)?<\/a><\/span><\/p>\n

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MSDW Processes\/Approvals<\/span><\/h2>\n

Q: How much are the Data Warehouse services?<\/a><\/span><\/p>\n

Q: Do I have to give a fund number?<\/a><\/span><\/p>\n

Q: What paperwork\/approvals do I need for an IRB research project?<\/a><\/span><\/p>\n

Q: What is the turnaround time for a custom data set?<\/a><\/span><\/p>\n

Q: Can I receive a cost and time estimate before agreeing to my data request?<\/a><\/span><\/p>\n

Q: Can I submit a recurring request?<\/a><\/span><\/p>\n

Q: Can I make changes to my data request requirements?<\/a><\/span><\/p>\n

Q: What if there is an issue with the data after my ticket has been closed?<\/a><\/span><\/p>\n

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Receiving Data<\/span><\/h2>\n

Q: When do I get my data?<\/a><\/span><\/p>\n

Q: How will my data be provided to me?<\/a><\/span><\/p>\n

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Data Sources<\/span><\/h2>\n

Q: What is Epic Clarity?<\/a><\/span><\/p>\n

Q: What is Epic Caboodle?<\/a><\/span><\/p>\n

Q: What is OMOP?<\/a><\/span><\/p>\n

Q: Where can I get more information about OMOP Data in MSDW?<\/a><\/span><\/p>\n

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User Support<\/span><\/h2>\n

Q: What are ways I can meet with the MSDW team to discuss my needs?<\/a><\/span><\/p>\n

Q: Who can I contact if I have questions?<\/a><\/span><\/p>\n

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<\/a>Q: How can I identify eligible cohorts available in MSDW?<\/span><\/p>\n

A:<\/strong><\/span> You can search the Mount Sinai Data Warehouse (MSDW) to identify eligible cohorts by using one of our de-identified self-service tools: Leaf, ATLAS, or TriNetX. Each tool has an accompanying tutorial for use. Click here <\/a> to learn more.<\/span><\/p>\n

<\/a>Q: What Data sources are available in the Data Warehouse?<\/span><\/span><\/p>\n

A:<\/strong><\/span> The majority of the data provided by the MSDW comes from the Epic (Verona, WI) electronic health record (EHR), which is the primary EHR for the Mount Sinai Health System (MSHS). Epic was implemented as the inpatient EHR at Mount Sinai Hospital (MSH) in late 2011. The MSDW provides researchers access to data on the over 12 million unique patients in the Mount Sinai Health System Epic EHR, of which nearly 5.5 million of these patients have had an encounter. In total there are over 115 million patient encounters recorded in Epic. The majority of the data collected by the MSDW comes from the Epic Clarity and Caboodle databases, as Epic is the primary electronic health record (EHR) across the Mount Sinai Health System (MSHS). The clinical data is extracted from the Epic Caboodle and Clarity databases, transformed to the OMOP Common Data Model (CDM) and is stored in the MSDW2 database. Epic data can be supplemented with other data resources, such as insurance information from MSX and endoscopy data from Provation.<\/span><\/p>\n

<\/a>Q: How far back does the data go?<\/span><\/p>\n

A:<\/strong><\/span> The majority of the data provided by the MSDW comes from the Epic (Verona, WI) electronic health record (EHR), which is the primary EHR for the Mount Sinai Health System (MSHS). Epic was implemented as the inpatient EHR at Mount Sinai Hospital (MSH) in late 2011. Subsequently, Epic has been implemented in additional inpatient facilities across the MSHS, including Mount Sinai Queens (2013), Mount Sinai West (2018), Mount Sinai St. Lukes (2018), Mount Sinai Brooklyn (2019) and Mount Sinai Beth Israel (2020).<\/span><\/p>\n

<\/a>Q: How often is the data refreshed?<\/span><\/span><\/p>\n

A:<\/strong><\/span> The data in the MSDW is refreshed nightly.<\/span><\/p>\n

<\/a>Q: What data is available in MSDW?<\/span><\/span><\/p>\n

A:<\/strong><\/span> MSDW data broadly includes clinical and operational data, specifically patient encounters and associated diagnoses; patient medical, surgical, social, family, and immunization histories; patient assessments; vitals; clinical orders including lab, radiology, pathology, and medications; medication administrations, clinical progress notes; and clinical discharge summaries. A vast majority of this data is drawn from Mount Sinai Health System\u2019s Epic EHR. Our Data Analysts can help you to determine what will work best for your research and ensure your requested data set is accurate and comprehensible.<\/span><\/p>\n

Also, please see our comprehensive list of data sources for more details here<\/a>.<\/span><\/p>\n

<\/a>Q: Does MSDW have de-identified and PHI data?<\/span><\/p>\n

A:<\/strong><\/span> MSDW contains PHI data, which is accessible with an approved IRB or QI documentation. Researchers requesting data without an IRB will receive de-identified data. The de-identified data set is provided with confirmation that the data have no HIPAA identifiers. Please note that the MSDW team does not offer de-identified health information in free text fields (such as progress notes). Click here<\/a> to learn more about the de-identified data service.<\/span><\/p>\n

<\/a>Q: What information is available in the Enterprise Data Catalog?<\/span><\/p>\n

A:<\/strong><\/span> The Informatica Enterprise Data Catalog is intended to include all three types of metadata about our OMOP databases in MSDW:<\/span><\/p>\n\n\n\n\n\n\n
Metadata Type<\/strong><\/td>\nAlternative Name<\/strong><\/td>\nDefinition<\/strong><\/td>\n<\/tr>\n
Technical<\/td>\nStructural<\/td>\nData that provides information about containers of data (documents, web pages, database tables)<\/td>\n<\/tr>\n
Business<\/td>\nDescriptive<\/td>\n\n
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  • Information about the business-meaning of data (e.g. description of a KPI)<\/li>\n
  • Data definitions (entities, attributes, elements)<\/li>\n<\/ul>\n<\/td>\n<\/tr>\n
Process<\/td>\nAdministrative<\/td>\n\n