696 lines
30 KiB
HTML
696 lines
30 KiB
HTML
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<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
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<div id="navbar" class="navbar-collapse collapse">
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<ul class="nav navbar-nav">
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Background
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="background.html">Model Background</a>
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</li>
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<li>
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<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
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</li>
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<li>
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<a href="vocabulary.html">How the Vocabulary is Built</a>
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</li>
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</ul>
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</li>
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<li class="dropdown">
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Conventions
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="dataModelConventions.html">General Conventions</a>
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</li>
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<li>
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<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
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</li>
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<li>
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<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
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</li>
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<a href="customConcepts.html">Custom Concepts</a>
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CDM Versions
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="cdm30.html">CDM v3.0</a>
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</li>
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<a href="cdm53.html">CDM v5.3</a>
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</li>
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<li class="dropdown-submenu">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">CDM v5.4</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="cdm54.html">CDM v5.4</a>
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</li>
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<li>
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<a href="cdm54Changes.html">Changes from CDM v5.3</a>
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</li>
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<li>
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<a href="cdm54erd.html">Entity Relationships</a>
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</li>
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<li>
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<a href="cdm54ToolingSupport.html">Detailed tooling support per CDM field</a>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-plus-square"></span>
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CDM Proposals
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
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</li>
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<li>
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<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
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</li>
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<li class="dropdown-submenu">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Accepted</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
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</li>
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</ul>
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</li>
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</ul>
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<span class="fa fa-question"></span>
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How to
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="download.html">Download the DDL</a>
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</li>
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<li>
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<a href="cdmRPackage.html">Use the CDM R Package</a>
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</li>
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<li>
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<a href="drug_dose.html">Calculate Drug Dose</a>
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</li>
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</ul>
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-life-ring"></span>
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Support
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
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</li>
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||
<li>
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||
<a href="faq.html">FAQ</a>
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||
</li>
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||
<li>
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||
<a href="sqlScripts.html">SQL Scripts</a>
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||
</li>
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||
<li>
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||
<a href="contribute.html">Ask a Question</a>
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||
</li>
|
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</ul>
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</li>
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||
</ul>
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<ul class="nav navbar-nav navbar-right">
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<li>
|
||
<a href="https://github.com/OHDSI/CommonDataModel">
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||
<span class="fa fa-github"></span>
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||
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</a>
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</li>
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</ul>
|
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</div><!--/.nav-collapse -->
|
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</div><!--/.container -->
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</div><!--/.navbar -->
|
||
|
||
<div id="header">
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||
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||
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<h1 class="title toc-ignore"><img src="ohdsi40x40.png"></img> OMOP
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Common Data Model</h1>
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</div>
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||
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<p>The Observational Medical Outcomes Partnership (OMOP) Common Data
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Model (CDM) is an open community data standard, designed to standardize
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the structure and content of observational data and to enable efficient
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analyses that can produce reliable evidence. A central component of the
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OMOP CDM is the OHDSI standardized vocabularies. The OHDSI vocabularies
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allow organization and standardization of medical terms to be used
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across the various clinical domains of the OMOP common data model and
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enable standardized analytics that leverage the knowledge base when
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constructing exposure and outcome phenotypes and other features within
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characterization, population-level effect estimation, and patient-level
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prediction studies.</p>
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<p>This website is meant to serve as a resource describing the
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specification of the available versions of the Common Data Model. This
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includes the structure of the model itself and the agreed upon
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conventions for each table and field as decided by the OHDSI Community.
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The vocabulary tables are part of the model and, as such, are detailed
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here. To download the vocabulary itself, please visit <a
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href="https://athena.ohdsi.org">https://athena.ohdsi.org</a>. For more
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||
information about the OHDSI suite of tools designed to implement best
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||
practices in characterization, population-level effect estimation and
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patient-level prediction, please visit <a
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||
href="https://ohdsi.github.io/Hades/">https://ohdsi.github.io/Hades/</a>.</p>
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||
<div id="the-cdm-working-group" class="section level2">
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||
<h2>The CDM Working Group</h2>
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||
<p>The CDM is managed by the OHDSI CDM Working Group. If you would like
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||
to join our group please fill out <a
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||
href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu">this
|
||
form</a> and check “Common Data Model” to be added to our Microsoft
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||
Teams environment. This working group endeavors to maintain the OMOP CDM
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||
as a living model by soliciting and responding to requests from the
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community based on use cases and research purposes. For more information
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||
on the CDM refresh process please see the description <a
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||
href="http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html">here</a>.
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You will find information on our meetings and links to join at the end
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||
of this page.</p>
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||
<div id="calendar" class="section level3">
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||
<h3>Calendar</h3>
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||
<p>This is the calendar of events for the CDM Working Group, including
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||
upcoming topics and links to meetings. If you would like to present to
|
||
the group regarding a new use case for the OMOP CDM or if you would like
|
||
the group’s assistance with a problem you are having, please fill out
|
||
our sign-up form.</p>
|
||
<p><a
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||
href="https://www.signupgenius.com/go/10C0948AEAD28A4F9CF8-workgroup"><img
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||
src="images/sign-up.png" style="width:15.0%" alt="Sign Up" /></a></p>
|
||
<p><strong>Note</strong> If you do you have access to the OHDSI Teams
|
||
Tenet, either contact Clair Blacketer at <a
|
||
href="mailto:mblacke@its.jnj.com" class="email">mblacke@its.jnj.com</a>
|
||
or fill out <a
|
||
href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu">this
|
||
form</a> and check “Common Data Model”</p>
|
||
<div class="toastui-calendar calendar html-widget html-fill-item-overflow-hidden html-fill-item" style="width:100%;height:600px;">
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<span id="htmlwidget-3c635e4b9afcc96376ef_menu_navi">
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<script type="application/json" data-for="htmlwidget-3c635e4b9afcc96376ef">{"x":{"options":{"defaultView":"month","useDetailPopup":true,"useFormPopup":false,"isReadOnly":true,"usageStatistics":false,"month":{"startDayOfWeek":1,"narrowWeekend":true},"calendars":[{"id":"1","name":"PERSO","color":"#000","backgroundColor":"#c6d19d","borderColor":"forestgreen"},{"id":"2","name":"WORK","color":"#000","backgroundColor":"#F5A9A9","borderColor":"firebrick"},{"id":"3","name":"COURSES","color":"#000","backgroundColor":"#c6e2f6","borderColor":"#3b7cc6"}]},"schedules":[{"category":"time","dueDateClass":"","id":"schedule098221f0e80498225150fa0e","calendarId":"1","title":"CDM WG Meeting","body":"","recurrenceRule":null,"start":"2023-01-03 10:00:00","end":"2023-01-03 11:00:00","location":"Teams: https://tinyurl.com/cdm1sttues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedulefa53cf7cc275fe7a83765d01","calendarId":"2","title":"CDM WG : 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11:00:00","location":"Teams: https://tinyurl.com/cdm1sttues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedule3d225bbc130266377d41cb66","calendarId":"2","title":"CDM WG Meeting","body":"","recurrenceRule":null,"start":"2023-05-16 13:00:00","end":"2023-05-16 14:00:00","location":"Teams: https://tinyurl.com/cdm3rdtues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedule03fb6abff396bfb3247abacc","calendarId":"1","title":"CDM WG Meeting","body":"","recurrenceRule":null,"start":"2023-06-06 10:00:00","end":"2023-06-06 11:00:00","location":"Teams: https://tinyurl.com/cdm1sttues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedulef685e426a598ccf225158b3e","calendarId":"2","title":"CDM WG Meeting","body":"","recurrenceRule":null,"start":"2023-07-18 13:00:00","end":"2023-07-18 14:00:00","location":"Teams: 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|
||
</div>
|
||
</div>
|
||
<div id="current-cdm-version" class="section level2">
|
||
<h2>Current CDM Version</h2>
|
||
<p>The current CDM version is <a
|
||
href="http://ohdsi.github.io/CommonDataModel/cdm54.html">CDM v5.4</a>,
|
||
depicted below. This CDM version was developed over the course of a year
|
||
by considering requests that were sent via our <a
|
||
href="https://github.com/OHDSI/CommonDataModel/issues">issues page</a>.
|
||
The list of proposed changes was then shared with the community in
|
||
multiple ways: through discussions at the weekly OHDSI Community calls,
|
||
discussions with the OHDSI Steering Committee, and discussions with all
|
||
potentially affected workgroups. The <a
|
||
href="http://ohdsi.github.io/CommonDataModel/cdm54Changes.html">final
|
||
changes</a> were then delivered to the Community through a new R package
|
||
designed to dynamically generate the DDLs and documentation for all
|
||
supported SQL dialects. Looking for an entity-relationshop diagram?
|
||
Click <a
|
||
href="http://ohdsi.github.io/CommonDataModel/cdm54erd.html">here</a>!</p>
|
||
<ul>
|
||
<li><a
|
||
href="https://github.com/OHDSI/CommonDataModel/tree/v5.4.0/inst/ddl/5.4">Link
|
||
to DDLs for CDM v5.4</a></li>
|
||
<li><a
|
||
href="https://github.com/OHDSI/CommonDataModel/tree/master#readme">Link
|
||
to ReadMe for instructions on how to use the R package</a></li>
|
||
</ul>
|
||
<p><img src="images/cdm54.png" /> <br></p>
|
||
<div id="current-support-for-cdm-v5.4" class="section level3">
|
||
<h3>Current Support for CDM v5.4</h3>
|
||
<p>The table below details which OHDSI tools support CDM v5.4. There are
|
||
two levels of support: legacy support means that the tool supports all
|
||
tables and fields that were present in CDM v5.3 and feature support
|
||
indicates that the tool supports any new tables and fields in CDM v5.4
|
||
that were not present in CDM v5.3. A green check ✔️ indicates that the
|
||
support level for the listed tool is in place, has been tested, and
|
||
released. A warning sign ❗ indicates that the support level for the
|
||
listed tool has been initiated but has not yet been tested and released.
|
||
<br></p>
|
||
<table>
|
||
<colgroup>
|
||
<col width="25%" />
|
||
<col width="25%" />
|
||
<col width="25%" />
|
||
<col width="25%" />
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="header">
|
||
<th><strong>Tool</strong></th>
|
||
<th><strong>Description</strong></th>
|
||
<th><strong>Legacy Support</strong></th>
|
||
<th><strong>Feature Support</strong></th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td><strong>CDM R package</strong></td>
|
||
<td>This package can be downloaded from <a
|
||
href="https://github.com/OHDSI/CommonDataModel/">https://github.com/OHDSI/CommonDataModel/</a>.
|
||
It functions to dynamically create the OMOP CDM documentation and DDL
|
||
scripts to instantiate the CDM tables.</td>
|
||
<td>✔️</td>
|
||
<td>✔️</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td><strong>Data Quality Dashboard</strong></td>
|
||
<td>This package can be downloaded from <a
|
||
href="https://github.com/OHDSI/DataQualityDashboard">https://github.com/OHDSI/DataQualityDashboard</a>.
|
||
It runs a set of > 3500 data quality checks against an OMOP CDM
|
||
instance and is required to be run on all databases prior to
|
||
participating in an OHDSI network research study.</td>
|
||
<td>✔️</td>
|
||
<td>❗</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td><strong>Achilles</strong></td>
|
||
<td>This package can be downloaded from <a
|
||
href="https://github.com/OHDSI/Achilles">https://github.com/OHDSI/Achilles</a>,
|
||
performing a set of broad database characterizations against an OMOP CDM
|
||
instance.</td>
|
||
<td>✔️</td>
|
||
<td>❗</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td><strong>ARES</strong></td>
|
||
<td>This package can be downloaded from <a
|
||
href="https://github.com/OHDSI/Ares">https://github.com/OHDSI/Ares</a>
|
||
and is designed to display the results from both the ACHILLES and
|
||
DataQualityDashboard packages to support data quality and
|
||
characterization research.</td>
|
||
<td>✔️</td>
|
||
<td>❗</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td><strong>ATLAS</strong></td>
|
||
<td>ATLAS is an open source software tool for researchers to conduct
|
||
scientific analyses on standardized observational data. <a
|
||
href="http://atlas-demo.ohdsi.org/">Demo</a></td>
|
||
<td>✔️</td>
|
||
<td>❗</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td><strong>Rabbit-In-A-Hat</strong></td>
|
||
<td>This package can be downloaded from <a
|
||
href="https://github.com/OHDSI/WhiteRabbit">https://github.com/OHDSI/WhiteRabbit</a>
|
||
and is an application for interactive design of an ETL to the OMOP
|
||
Common Data Model with the help of the the scan report generated by
|
||
White Rabbit.</td>
|
||
<td>✔️</td>
|
||
<td>✔️</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td><strong>Feature Extraction</strong></td>
|
||
<td>This package can be downloaded from <a
|
||
href="https://github.com/OHDSI/FeatureExtraction">https://github.com/OHDSI/FeatureExtraction</a>.
|
||
It is designed to generate features (covariates) for a cohort generated
|
||
using the OMOP CDM.</td>
|
||
<td>✔️</td>
|
||
<td>✔️*</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td><strong>Cohort Diagnostics</strong></td>
|
||
<td>This package can be downloaded from <a
|
||
href="https://github.com/OHDSI/CohortDiagnostics">https://github.com/OHDSI/CohortDiagnostics</a>
|
||
and is used to critically evaluate cohort phenotypes.</td>
|
||
<td>✔️</td>
|
||
<td>❗</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p><br> * The <strong>Feature Extraction</strong> package supports all
|
||
relevant new features in CDM v5.4. For example, it was decided that,
|
||
from a methodological perspective, the EPISODE and EPISODE_EVENT tables
|
||
should not be included to define cohort covariates because the events
|
||
that make up episodes are already pulled in as potential covariates.</p>
|
||
<p><br></p>
|
||
</div>
|
||
<div id="cdm-wg-important-links" class="section level3">
|
||
<h3>CDM WG Important Links</h3>
|
||
<ul>
|
||
<li><a
|
||
href="https://drive.google.com/open?id=1DaNKe6ivIAZPJeI31VJ-pzNB9wS9hDqu">Google
|
||
Drive Location</a></li>
|
||
<li><a
|
||
href="https://docs.google.com/document/d/1WgKePjrI_cGdqn2XQCe1JdGaTzdMqU4p5ihkMt8fcAc/edit?usp=sharing">Running
|
||
Agenda</a></li>
|
||
<li><a href="https://github.com/OHDSI/CommonDataModel">CDM
|
||
Github</a></li>
|
||
<li><a
|
||
href="http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html">Process
|
||
for adopting CDM and Vocabulary changes</a></li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
</div>
|
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|
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