{"id":7218,"date":"2023-05-24T14:24:28","date_gmt":"2023-05-24T18:24:28","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/minervalab\/?page_id=7218"},"modified":"2024-10-21T10:53:38","modified_gmt":"2024-10-21T14:53:38","slug":"mount-sinai-data-warehouse-msdw-de-identified-omop-data-set","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/minervalab\/resources\/data-ark\/mount-sinai-data-warehouse-msdw-de-identified-omop-data-set\/","title":{"rendered":"Mount Sinai Data Warehouse (MSDW) de-identified OMOP Data Set"},"content":{"rendered":"

[et_pb_section fb_built=”1″ fullwidth=”on” _builder_version=”4.9.0″ _module_preset=”default”][et_pb_fullwidth_menu menu_id=”14″ menu_style=”centered” fullwidth_menu=”on” active_link_color=”#d80b8c” dropdown_menu_bg_color=”#221f72″ dropdown_menu_line_color=”#221f72″ dropdown_menu_active_link_color=”#d80b8c” _builder_version=”4.9.0″ _module_preset=”default” menu_font=”|600|||||||” menu_text_color=”#FFFFFF” menu_font_size=”16px” background_color=”#221f72″ background_layout=”dark” sticky_position=”top”][\/et_pb_fullwidth_menu][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.9.0″ _module_preset=”default” custom_padding=”0px||0px||false|false”][et_pb_row _builder_version=”4.9.0″ _module_preset=”default” custom_padding=”||0px||false|false”][et_pb_column type=”4_4″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_text admin_label=”Breadcrumb” _builder_version=”4.9.0″ _module_preset=”default”]<\/p>\n

Scientific Computing and Data<\/a> \/ Research Data Services<\/a> \/\u00a0Data Ark: Data Commons<\/a> \/ OMOP<\/a><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ admin_label=”section” _builder_version=”4.9.0″ custom_padding=”0px||||false|false”][et_pb_row _builder_version=”4.9.0″ _module_preset=”default” custom_margin=”|auto|-12px|auto||”][et_pb_column type=”4_4″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_text admin_label=”Header” _builder_version=”4.9.0″ _module_preset=”default” header_font=”|700|||||||” header_text_color=”#221f72″ hover_enabled=”0″ sticky_enabled=”0″]<\/p>\n

Mount Sinai Data Warehouse (MSDW) De-identified OMOP Data Set<\/span><\/strong><\/h1>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.9.0″ _module_preset=”default” custom_margin=”|auto|-12px|auto||”][et_pb_column type=”4_4″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_text admin_label=”Header” _builder_version=”4.9.0″ _module_preset=”default” header_font=”|700|||||||” header_text_color=”#221f72″ hover_enabled=”0″ sticky_enabled=”0″][\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_5,3_5,1_5″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_column type=”1_5″ _builder_version=”4.9.0″ _module_preset=”default”][\/et_pb_column][et_pb_column type=”3_5″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_image src=”https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2023\/05\/OMOP.png” title_text=”OMOP” _builder_version=”4.9.0″ _module_preset=”default” custom_margin=”-37px|||||”][\/et_pb_image][\/et_pb_column][et_pb_column type=”1_5″ _builder_version=”4.9.0″ _module_preset=”default”][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.9.0″ _module_preset=”default” custom_margin=”|auto|35px|auto||” custom_padding=”28px|||||”][et_pb_column type=”4_4″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_text admin_label=”Text” _builder_version=”4.9.0″ _module_preset=”default” text_line_height=”1.5em”]<\/p>\n

Overview<\/h2>\n

The Mount Sinai Data Warehouse (MSDW) collects clinical and operational data for use in clinical and translational research, as well as quality improvement initiatives.<\/p>\n

The MSDW de-identified OMOP (Observational Medical Outcomes Partnership) Data Set is the entire copy for MSDW OMOP data mart extracted from their SQL database. \u00a0It contains over 11 million patient records and over 87 million patient encounters (as of September 2021, see\u00a0Data Sources<\/a>\u00a0for more details).<\/p>\n

MSDW ecosystem uses the Observational Health Data Sciences and Informatics (OHDSI) collaborative\u2019s\u00a0OMOP Common Data Model<\/a>\u00a0to facilitate optimal data sharing and interoperability both internally (at Mount Sinai) and externally with research partners. The data collected by MSDW are extracted from Mount Sinai\u2019s Epic Caboodle database and other ancillary systems, which includes demographics, encounters, labs, conditions, diagnoses, medications and more. The data is transformed to the OMOP Common Data Model (CDM) format and loaded to the MSDW database. Reference OHDSI\u2019s\u00a0data dictionary<\/a>\u00a0for OMOP CDM.<\/p>\n

Access<\/h2>\n

To use these data, you must read, agree and sign the Data User Agreement<\/a> (you must be logged in through the Mount Sinai campus network\/secure remote VPN and a Minerva HPC account is needed). On Minerva, you can load module $ module load dataark <\/strong>to see the path variables.<\/p>\n

More information<\/h2>\n

Please visit MSDW page and open a ticket<\/a> .<\/p>\n

Helpful External Web Sites<\/h2>\n

“Why use the OMOP CDM?” from OHDSI.org: https:\/\/www.ohdsi.org\/wp-content\/uploads\/2014\/07\/Why-CDM.png<\/a>. Retrieved May 22, 2023.<\/p>\n

Data Ark Data Sets<\/h2>\n

Please visit the Data Ark Data Set<\/a> webpage to explore other data sets.[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

Scientific Computing and Data \/ Research Data Services \/\u00a0Data Ark: Data Commons \/ OMOPMount Sinai Data Warehouse (MSDW) De-identified OMOP Data SetOverview The Mount Sinai Data Warehouse (MSDW) collects clinical and operational data for use in clinical and translational research, as well as quality improvement initiatives. The MSDW de-identified OMOP (Observational Medical Outcomes Partnership) Data […]<\/p>\n","protected":false},"author":600,"featured_media":0,"parent":1321,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-7218","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/7218","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/users\/600"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/comments?post=7218"}],"version-history":[{"count":20,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/7218\/revisions"}],"predecessor-version":[{"id":8462,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/7218\/revisions\/8462"}],"up":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/1321"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/media?parent=7218"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}