[\/et_pb_text][et_pb_text admin_label=”Tutorial” _builder_version=”4.9.0″ header_text_color=”#221f72″ header_3_text_color=”#00aeef” background_size=”initial” background_position=”top_left” background_repeat=”repeat” hover_enabled=”0″ sticky_enabled=”0″]<\/p>\n
Leaf Tutorial<\/h1>\n
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You can use Leaf<\/a> to query de-identified data in the Mount Sinai Data Warehouse (MSDW) 2.0. Leaf is \u201ca lightweight drag-and-drop web application that enables direct querying of arbitrary clinical databases\u201d (Dobbins,\u00a02019<\/a>).<\/p>\n User Access<\/a> <\/p>\n All Mount Sinai users can access Leaf using School or Hospital login credentials:<\/p>\n <\/p>\n <\/p>\n All Leaf users must register for user accounts. Attempts to sign in without enabled accounts will be blocked from entry (see Figure 1).<\/p>\n Figure 1: Login error for users that are not registered Leaf users<\/p><\/div>\n <\/p>\n <\/p>\n To access Leaf and begin querying MSDW,\u00a0log\u00a0in to\u00a0Leaf<\/a>.<\/p>\n <\/p>\n <\/p>\n Access Leaf through the Mount Sinai network. Access from campus directly\u00a0or through a VPN tunnel using valid Mount Sinai credentials.<\/p>\n Note: if you have not used Leaf previously or your Mount Sinai login session to Leaf has timed out, you will be prompted to log in through a Microsoft<\/em> service that Mount Sinai uses to manage user credentials (see Figure 2).<\/em><\/p>\n Figure 2: Leaf Sign-in (if Mount Sinai session has timed out)<\/p><\/div>\n <\/p>\n <\/p>\n Leaf’s landing page asks for preliminary information:<\/p>\n Figure 3: Selection path to access De-Identified Patient Data for Research without an IRB<\/p><\/div>\n <\/p>\n <\/p>\n Leaf enables you to quickly select patients who satisfy criteria from multiple medical and other domains. There are several key areas of the Leaf user interface:<\/p>\n Figure 4: Leaf landing page<\/p><\/div>\n Need Help? In the left-hand navigation column (#6 in the landing page), scroll to the bottom of the page and select the \u201cNeed Help\u201d button to review assistance options, including directions to submit a ticket.<\/p>\n <\/p>\n Leaf\u00a0initially\u00a0opens to the left-hand menu tab to \u201cFind Patients\u201d\u00a0where\u00a0you can run your search query.<\/p>\n <\/p>\n <\/p>\n Concepts with numerical values–such as Lab Results, Vitals, and Age–can all be refined by numerical parameters. To set them, select the arrow to the right of each filter. For example, search for living adults by adding Demographics: Age\u00a0<\/strong>to the top box (filtering for Greater Than or Equal to 18) and\u00a0Vital Status: Living\u00a0<\/strong>to the bottom half of the same box under \u201cIn the Same Encounter\u201d (see Figure 5)<\/p>\n Figure 5: Adding Living Adults (age 64 or younger) parameters to the query, then removing an aspect<\/p><\/div>\n <\/p>\n Identify up to two additional Concepts to drag and drop into the adjacent query boxes.\u00a0Query box filters can adjust to custom date range,\u00a0frequency, or inclusion\/exclusion\u00a0by selecting the arrow to the right of each filter.<\/p>\n \u00a0<\/strong><\/p>\n <\/p>\n Above the Concepts tree is a search bar in which you can enter keywords to quickly find concepts which contain your terms (see Figure 6)<\/p>\n Figure 6: Searching for specific Concepts<\/p><\/div>\n <\/p>\n <\/p>\n Remove any concept from the query boxes by clicking on it and dragging it out of the query box to anywhere else on the page. This will remove the concept from your search or enable you to replace it with a different one.<\/p>\n After\u00a0your\u00a0search criteria is established, click the green button to\u00a0\u201cRun\u00a0Query<\/strong>\u201d\u00a0and review results.\u00a0Note: Leaf results larger than 200,000 patients will not display Visualization or Patient List data.<\/em><\/p>\n <\/p>\n <\/p>\n Age:<\/strong> Patient age always refers to the patient\u2019s age at the time a query runs. This means the same patients may not consistently appear in age-related searches that you run on different days, and that age may not correlate to the date of patient\u2019s vitals. For example, a record for a patient born on January 1, 2000 will not appear in searches of Age: > 18 when queried on January 1, 2017, but will appear in the same search when queried after January 1, 2019.<\/p>\n Age, Race, Gender, and Ethnicity<\/strong>: these are considered immutable patient characteristics. Immutable patient characteristics are denoted by an orange human icon (see Figure 6). These characteristics cannot be combined with Encounter concepts in one query box. Doing so produces a search error (see Figure 7).<\/p>\n Figure 7: Query Error (Combined immutable characteristics with encounter concept in the same query box)<\/p><\/div>\n <\/p>\n Encounter:<\/strong> An Encounter, Visit, or ICD-10-CM Condition represents patient data obtained on a specific date. Such data is denoted by a blue clock icon (refer to Figure 8). This data can include Conditions<\/strong> (diagnoses), Procedures <\/strong>(CPT Concept), Encounters<\/strong>, Labs<\/strong>, and Vitals<\/strong>.<\/p>\n Encounter <\/strong>concepts cannot be combined with Immutable Characteristics in a panel. Immutable characteristics are defined by present date, whereas Encounter concepts are defined by date recorded<\/p>\n Figure 8: immutable characteristics with orange human icons<\/p><\/div>\n ICD-10-CM Conditions: <\/strong>Conditions are structured in a tree format. Pulling one condition into a query will also pull all subsequent nodes in that tree structure. For example, searching for \u201cMigraine (ICD10CM:G43.001-G43.D1)\u201d will query for the \u201cMigraine\u201d condition and <\/em>for all lower nodes in the tree as depicted in the red box in Figure 9. However, searching for a terminal node in a tree, for example \u201cMigraine with aura, not intractable, with status migrainosis\u201d (as depicted in orange), the search will query for only that condition.<\/p>\n Figure 9: Node hierarchy in a condition tree<\/p><\/div>\n \u00a0<\/strong><\/p>\n Current Procedural Terminology Concept: <\/strong>Services, procedures, and events are structured in a tree format (similar to Conditions). These elements can also be located by typing a specific Procedure Term in the search box.<\/p>\n <\/p>\n Vitals: <\/strong>Vital concepts rely on units of measurement, specifically:<\/p>\n <\/p>\n Search Logic:<\/strong> Leaf query boxes are connected by logical \u201cand\u201d operations where all concepts must be satisfied. For example, a search can find patients who are at least age 55, female, and white (see Figure 10) meeting all these criteria.<\/p>\n Within a query box, multiple alternatives can be connected by logical \u201cor\u201d operations. For example, a search can find patients who are male and are either Black\/African American or Hispanic\/Latino (see Figure 11).<\/p>\n Figure 10: Age, Gender, Race Query<\/p><\/div> Figure 11: Gender, Ethnicity either\/or Query<\/p><\/div><\/p>\n <\/p>\n Search Logic And Not:<\/strong> Extending search logic, adjusting query language to \u201cAnd Not\u201d to eliminate variables from the query will turn the \u201cAnd Not\u201d query box red (see Figure 12).<\/p>\n Figure 12: And Not Logic<\/p><\/div>\n Note: a red query box specifies \u201cAnd Not\u201d logic, not a query error.<\/em><\/p>\n <\/p>\n Search Logic In Same Encounter:<\/strong> Combine concepts in the same panel to query for encounters, conditions, or vitals measured at the same time (in the same encounter). Observe the difference between examples 1 and 2 below:<\/p>\n Figure 13: Query of Migraine and Emergency Room Visit<\/p><\/div> Figure 14: Query of Migraine and ER Visit in Same Encounter<\/p><\/div><\/p>\n <\/p>\n Date Logic: <\/strong>Query boxes can specify encounter date to include custom date ranges, including today, in the last 7 days or 30 days, or within a custom date range.<\/p>\n Dates <\/strong>can adjust. Use drop-down menus in the blue header of any box to specify the relative date of another encounter (such as \u201cIn the Same Encounter\u201d and \u201cWithin +\/-\u201c or \u201cIn the following\u2026\u201d time period) to customize a time frame for the query.<\/p>\n <\/p>\n <\/p>\n Leaf provides a quick data overview with customizable options for review. From the left-hand navigation:<\/p>\n Select a tab to view the information.<\/p>\n \u00a0<\/strong><\/p>\n <\/p>\n Select the menu for \u201cBasic Demographics\u201d to add or remove fields from the dataset (see Figure 15)<\/p>\n Figure 15: Selecting columns for data set<\/p><\/div>\n <\/p>\n Reorder columns by clicking and dragging column position on the dataset.<\/p>\n \u00a0<\/strong><\/p>\n <\/p>\n After establishing dataset\u00a0criteria, click the green button to \u201cExport\u00a0Data<\/strong>\u201d<\/p>\n <\/p>\n <\/p>\n Datasets can be saved as a local file, and search queries can be saved within Leaf.<\/p>\n Figure 16: Saved Queries, Open and Delete<\/p><\/div>\n <\/p>\n <\/p>\n See other resources for Leaf:<\/p>\n <\/p>\n [\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":" Scientific Computing and Data\u00a0\/\u00a0Mount Sinai Data Warehouse \/ Tutorials \/ Leaf TutorialLeaf Tutorial You can use Leaf to query de-identified data in the Mount Sinai Data Warehouse (MSDW) 2.0. Leaf is \u201ca lightweight drag-and-drop web application that enables direct querying of arbitrary clinical databases\u201d (Dobbins,\u00a02019). Table of Contents User AccessAccess ErrorLog In to LeafSecure […]<\/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":" You can use Leaf<\/a> to query the data in\u00a0the\u00a0Mount Sinai Data Warehouse (MSDW) 2.0.\u00a0Leaf is \u201ca lightweight drag-and-drop web application that enables direct querying of arbitrary clinical databases\u201d\u00a0(Dobbins,\u00a02019<\/a>).<\/p> \u00a0<\/p> First-time Leaf users must request\u00a0access.<\/p> \u00a0<\/p> Once you receive an email confirmation that your account is set up:<\/p> \u00a0<\/p> All Leaf users must be granted administrative access. Attempts to sign in without having administrative permission will be blocked from entry (see Figure 1).<\/p>[caption id=\"\" align=\"alignnone\" width=\"518\"] \u00a0<\/p> To access Leaf and begin querying MSDW,\u00a0log\u00a0in to\u00a0Leaf<\/a><\/p> \u00a0<\/p> Access Leaf through the Mount Sinai network. Access from campus directly\u00a0or through a VPN tunnel using valid Mount Sinai credentials.<\/p> Note:\u00a0if you\u00a0have not used Leaf previously or your\u00a0Mount Sinai login session\u00a0to Leaf\u00a0has timed out,\u00a0you\u00a0will\u00a0be\u00a0prompted\u00a0to log in\u00a0through Microsoft<\/em> (see Figure 2).<\/em><\/p>[caption id=\"\" align=\"alignnone\" width=\"503\"] \u00a0<\/p> Leaf's landing page asks for preliminary information:<\/p> \u00a0<\/p> \u00a0<\/p> Leaf enables you to quickly search for de-identified patient records\u00a0and data\u00a0using dynamic search criteria.\u00a0There are several key areas in Leaf:<\/p>[caption id=\"\" align=\"alignnone\" width=\"1393\"]\n
Table of Contents<\/h3>\n
Access Error<\/a>
Log In to Leaf<\/a>
Secure Access<\/a>
Select Usage Information<\/a>
Leaf Overview<\/a>
Constructing Queries<\/a>
Specify Query Parameters<\/a>
Search for Concepts<\/a>
Remove Concepts<\/a>
Clinical Domain Details: Query Parameters<\/a>
Viewing Search Results<\/a>
Exporting Data<\/a>
Saving Search Results<\/a>
Additional Resources<\/a><\/p>\n<\/blockquote>\n<\/a>User Access<\/h3>\n
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<\/a>Access Error<\/h3>\n
![\"Figure](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/08\/Leaf_Doc_01.jpg\")
<\/a>Log in to Leaf<\/h3>\n
<\/a>Secure Access<\/h3>\n
![\"Figure](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/08\/Leaf_Doc_02.jpg\")
<\/a>Select Usage Information<\/h3>\n
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![\"Figure](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/08\/Leaf_Doc_03.jpg\")
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<\/a>Leaf Overview<\/h3>\n
![\"\"](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2022\/05\/image009-1024x475.png\")
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<\/a>Constructing Queries<\/h3>\n
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The acronyms in parentheses indicate the standardized medical vocabulary used to encode each clinical domain.<\/li>\n![](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/08\/Leaf_Doc_Demographics.jpg\")
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<\/a>Specify Query Parameters<\/h3>\n
![\"\"](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2022\/06\/Leaf-query-demo-02.gif\")
<\/a>Search for Concepts<\/h3>\n
![\"\"](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/09\/image017_2.png\")
<\/a>Remove Concepts<\/h3>\n
<\/a>Clinical Domain Details: Query Parameters<\/h3>\n
![\"Figure](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/08\/Leaf_Doc_07.jpg\")
![\"\"](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/09\/image021_2.png\")
![\"Figure](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/10\/image009_2.png\")
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![\"\"](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/09\/image018_2.png\")
![\"\"](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/09\/imagge018_3.png\")
![\"Figure](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/08\/Leaf_Doc_12.jpg\")
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![\"Figure](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/08\/Leaf_Doc_13.jpg\")
![\"Figure](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/08\/Leaf_Doc_14.jpg\")
Viewing Search Results<\/a><\/h3>\n
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<\/a>Viewing Results<\/h3>\n
![\"\"](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/10\/image015_2-300x194.png\")
<\/a>Exporting Data<\/h3>\n
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<\/a>Saving Search Results<\/h3>\n
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![\"Figure](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/08\/Leaf_Doc_16_2.jpg\")
<\/a>Additional Resources<\/h3>\n
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SET UP USER ACCESS<\/strong><\/h2>
ACCESS ERROR<\/strong><\/h2>
Figure 1: Login error for users with unverified accounts[\/caption]LOG IN TO LEAF<\/strong><\/h1>
SECURE ACCESS\u00a0\u00a0<\/strong><\/h2>
Figure 2: Leaf Sign-in (if Mount Sinai session has timed out)[\/caption]SELECT\u00a0USAGE\u00a0INFORMATION<\/strong><\/h2>
Figure 3: Selection path to access De-Identified Patient Data for Research without an IRB[\/caption]LEAF OVERVIEW<\/strong><\/h1>
![\"Figure](\"https:\/\/labs.icahn.mssm.edu\/msdw\/wp-content\/uploads\/sites\/350\/2021\/09\/image011.png\")
Figure 4: Leaf Overview[\/caption]