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<title>OMOP CDM Frequently Asked Questions</title>
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<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
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<script src="site_libs/header-attrs-2.13/header-attrs.js"></script>
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<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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h6 {font-size: 12px;}
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code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
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pre:not([class]) { background-color: white }</style>
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<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
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<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
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<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
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<script src="site_libs/navigation-1.1/tabsets.js"></script>
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<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
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<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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<link rel="stylesheet" href="style.css" type="text/css" />
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summary {
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}
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details > summary > p:only-child {
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display: inline;
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pre code {
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<style type="text/css">
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#TOC {
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margin: 25px 0px 20px 0px;
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}
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@media (max-width: 768px) {
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#TOC {
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position: relative;
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width: 100%;
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}
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}
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@media print {
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.toc-content {
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/* see https://github.com/w3c/csswg-drafts/issues/4434 */
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float: right;
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}
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}
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.toc-content {
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padding-left: 30px;
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padding-right: 40px;
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}
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div.main-container {
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max-width: 1200px;
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}
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div.tocify {
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width: 20%;
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max-width: 260px;
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max-height: 85%;
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}
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@media (min-width: 768px) and (max-width: 991px) {
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div.tocify {
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width: 25%;
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}
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@media (max-width: 767px) {
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div.tocify {
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}
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border-radius: 0px;
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}
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</style>
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</head>
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<div class="container-fluid main-container">
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<div class="row">
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<div class="col-xs-12 col-sm-4 col-md-3">
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<div id="TOC" class="tocify">
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</div>
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</div>
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<div class="toc-content col-xs-12 col-sm-8 col-md-9">
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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<div class="container">
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<div class="navbar-header">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
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</a>
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<span class="fa fa-landmark"></span>
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Background
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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" aria-expanded="false">
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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-list-alt"></span>
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Conventions
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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" aria-expanded="false">
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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-history"></span>
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CDM Versions
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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" aria-expanded="false">NEW CDM v5.4</a>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">NEW 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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</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" aria-expanded="false">
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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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Proposals
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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" aria-expanded="false">Accepted</a>
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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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</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" aria-expanded="false">
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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-question"></span>
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How to
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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" aria-expanded="false">
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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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<p>OHDSI runs as a distributed data network. All analyses are publicly available and can be downloaded to run at each site. The packages can be run locally and, at the data partner’s discretion, aggregate results can be shared with the study coordinator.</p>
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<p>Data partners can also make use of one of OHDSI’s open-source tools called <a href="https://github.com/OHDSI/arachne">ARACHNE</a>, a tool to facilitate distributed network analytics against the OMOP CDM.</p>
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</div>
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<div id="recommended-system-requirements" class="section level2">
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<h2>Recommended System Requirements</h2>
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<p>It is difficult to recommend what technical capabilities a site needs to set up an ETL because it is heavily dependent on the amount of data they have and how they plan to use it. Here are some examples of options that have worked well for small to medium organizations and large organizations:</p>
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<p><strong>Small-to-Medium Organization</strong></p>
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<ul>
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<li>CDM size is 100MB to several GBs</li>
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<li>Vocab ~20GB</li>
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<li>Results < 500 MB</li>
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<li>Recommend
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<ul>
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<li>Server class machine disk >= 250GB (SSD preferred), >= 4 cores, >= 32GB RAM</li>
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</ul></li>
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</ul>
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<p><strong>Large Organization</strong></p>
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<ul>
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<li>CDM size is 12GB to several TBs</li>
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<li>Vocab ~20GB</li>
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<li>Results < 500 MB</li>
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<li>Recommend
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<ul>
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<li>Cloud-based infrastructure like multiple AWS Redshift clusters, for example:</li>
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<li><img src="images/AWS_clusters.png" /></li>
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</ul></li>
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</ul>
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</div>
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</div>
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</div>
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</div>
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<!-- code folding -->
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<script>
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$(document).ready(function () {
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// temporarily add toc-ignore selector to headers for the consistency with Pandoc
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$('.unlisted.unnumbered').addClass('toc-ignore')
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// move toc-ignore selectors from section div to header
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$('div.section.toc-ignore')
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.removeClass('toc-ignore')
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.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
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// establish options
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var options = {
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hashGenerator: function (text) {
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return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
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scrollTo: 0
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};
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options.showAndHide = true;
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options.smoothScroll = true;
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// tocify
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var toc = $("#TOC").tocify(options).data("toc-tocify");
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});
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</script>
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<title>index.knit</title>
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<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
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<script src="site_libs/header-attrs-2.13/header-attrs.js"></script>
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<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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<link rel="stylesheet" href="style.css" type="text/css" />
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summary {
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display: list-item;
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}
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details > summary > p:only-child {
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display: inline;
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}
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pre code {
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padding: 0;
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}
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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<div class="container">
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<div class="navbar-header">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
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</a>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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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-landmark"></span>
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Background
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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" aria-expanded="false">
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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-list-alt"></span>
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Conventions
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</ul>
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</li>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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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-history"></span>
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CDM Versions
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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" aria-expanded="false">NEW CDM v5.4</a>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">NEW 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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</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" aria-expanded="false">
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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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Proposals
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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" aria-expanded="false">Accepted</a>
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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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</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" aria-expanded="false">
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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-question"></span>
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How to
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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" aria-expanded="false">
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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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<p>The CDM working group meets the first and third Tuesday of the month. See below for links to the meetings.</p>
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<p><strong>Every first Tuesday of the month at 1pm est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d">Teams Meeting</a></p>
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<p><strong>Every third Tuesday of the month at 1pm est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1611000164347?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%223c193b7f-c2ab-4bcf-b88c-f89a6b1fba38%22%7d">Teams Meeting</a></p>
|
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<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 [this form] (<a href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu" class="uri">https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu</a>) and check “Common Data Model”</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>
|
||||
<div id="cdm-wg-important-links" class="section level3">
|
||||
<h3>CDM WG Important Links</h3>
|
||||
|
|
|
|||
28
rmd/faq.Rmd
28
rmd/faq.Rmd
|
|
@ -1,11 +1,12 @@
|
|||
---
|
||||
title: "OMOP CDM Frequently Asked Questions"
|
||||
output:
|
||||
html_document
|
||||
|
||||
html_document:
|
||||
toc: yes
|
||||
toc_depth: 5
|
||||
toc_float: yes
|
||||
---
|
||||
|
||||
|
||||
**1. I understand that the common data model (CDM) is a way of organizing disparate data sources into the same relational database design, but how can it be effective since many databases use different coding schemes?**
|
||||
|
||||
During the extract, transform, load (ETL) process of converting a data source into the OMOP common data model, we standardize the structure (e.g. tables, fields, data types), conventions (e.g. rules that govern how source data should be represented), and content (e.g. what common vocabularies are used to speak the same language across clinical domains). The common data model preserves all source data, including the original source vocabulary codes, but adds the standardized vocabularies to allow for network research across the entire OHDSI research community.
|
||||
|
|
@ -171,3 +172,24 @@ Queries are written in R and SQL. The [SqlRender](https://github.com/OHDSI/sqlre
|
|||
OHDSI runs as a distributed data network. All analyses are publicly available and can be downloaded to run at each site. The packages can be run locally and, at the data partner’s discretion, aggregate results can be shared with the study coordinator.
|
||||
|
||||
Data partners can also make use of one of OHDSI's open-source tools called [ARACHNE](https://github.com/OHDSI/arachne), a tool to facilitate distributed network analytics against the OMOP CDM.
|
||||
|
||||
## Recommended System Requirements
|
||||
|
||||
It is difficult to recommend what technical capabilities a site needs to set up an ETL because it is heavily dependent on the amount of data they have and how they plan to use it. Here are some examples of options that have worked well for small to medium organizations and large organizations:
|
||||
|
||||
**Small-to-Medium Organization**
|
||||
|
||||
- CDM size is 100MB to several GBs
|
||||
- Vocab ~20GB
|
||||
- Results < 500 MB
|
||||
- Recommend
|
||||
- Server class machine disk >= 250GB (SSD preferred), >= 4 cores, >= 32GB RAM
|
||||
|
||||
**Large Organization**
|
||||
|
||||
- CDM size is 12GB to several TBs
|
||||
- Vocab ~20GB
|
||||
- Results < 500 MB
|
||||
- Recommend
|
||||
- Cloud-based infrastructure like multiple AWS Redshift clusters, for example:
|
||||
- 
|
||||
|
|
|
|||
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|
|
@ -51,8 +51,7 @@ The CDM working group meets the first and third Tuesday of the month. See below
|
|||
**Every third Tuesday of the month at 1pm est** [Teams Meeting](https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1611000164347?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%223c193b7f-c2ab-4bcf-b88c-f89a6b1fba38%22%7d)
|
||||
|
||||
|
||||
**Note** If you do you have access to the OHDSI Teams Tenet, either contact Clair Blacketer at mblacke@its.jnj.com or fill out [this form]
|
||||
(https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu) and check "Common Data Model"
|
||||
**Note** If you do you have access to the OHDSI Teams Tenet, either contact Clair Blacketer at mblacke@its.jnj.com or fill out [this form](https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu) and check "Common Data Model"
|
||||
|
||||
### CDM WG Important Links
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue