2019-10-31 19:06:09 +00:00
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<!DOCTYPE html>
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2020-04-27 20:35:41 +00:00
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<html>
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2019-10-31 19:06:09 +00:00
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<head>
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<meta charset="utf-8" />
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<meta name="generator" content="pandoc" />
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2020-04-27 20:35:41 +00:00
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<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
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2019-10-31 19:06:09 +00:00
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2023-02-08 20:04:22 +00:00
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<title> OMOP CDM Background</title>
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2019-10-31 19:06:09 +00:00
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2023-10-26 18:13:30 +00:00
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<script src="site_libs/header-attrs-2.25/header-attrs.js"></script>
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2022-01-13 18:59:03 +00:00
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<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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2019-10-31 19:06:09 +00:00
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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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<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
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<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
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<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
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2022-01-13 18:59:03 +00:00
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<style>h1 {font-size: 34px;}
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h1.title {font-size: 38px;}
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h2 {font-size: 30px;}
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h3 {font-size: 24px;}
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h4 {font-size: 18px;}
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h5 {font-size: 16px;}
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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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2023-10-26 18:13:30 +00:00
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<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
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2019-10-31 19:06:09 +00:00
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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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2023-10-26 18:13:30 +00:00
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<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
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<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
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2019-10-31 19:06:09 +00:00
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<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
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2021-01-06 15:52:57 +00:00
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<style type="text/css">
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code{white-space: pre-wrap;}
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span.smallcaps{font-variant: small-caps;}
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span.underline{text-decoration: underline;}
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div.column{display: inline-block; vertical-align: top; width: 50%;}
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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ul.task-list{list-style: none;}
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</style>
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2019-10-31 19:06:09 +00:00
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<style type="text/css">code{white-space: pre;}</style>
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<script type="text/javascript">
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if (window.hljs) {
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hljs.configure({languages: []});
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hljs.initHighlightingOnLoad();
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if (document.readyState && document.readyState === "complete") {
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window.setTimeout(function() { hljs.initHighlighting(); }, 0);
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}
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}
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</script>
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2021-01-06 15:52:57 +00:00
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2022-07-27 01:48:28 +00:00
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2019-10-31 19:06:09 +00:00
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<link rel="stylesheet" href="style.css" type="text/css" />
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<style type = "text/css">
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.main-container {
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max-width: 940px;
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margin-left: auto;
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margin-right: auto;
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}
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img {
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max-width:100%;
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}
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.tabbed-pane {
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padding-top: 12px;
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}
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.html-widget {
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margin-bottom: 20px;
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}
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button.code-folding-btn:focus {
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outline: none;
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}
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summary {
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display: list-item;
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}
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2022-07-27 01:48:28 +00:00
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details > summary > p:only-child {
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display: inline;
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}
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2022-01-13 18:59:03 +00:00
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pre code {
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padding: 0;
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}
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2019-10-31 19:06:09 +00:00
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</style>
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<style type="text/css">
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.dropdown-submenu {
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position: relative;
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}
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.dropdown-submenu>.dropdown-menu {
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top: 0;
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left: 100%;
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margin-top: -6px;
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margin-left: -1px;
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border-radius: 0 6px 6px 6px;
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}
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.dropdown-submenu:hover>.dropdown-menu {
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display: block;
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}
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.dropdown-submenu>a:after {
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display: block;
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content: " ";
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float: right;
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width: 0;
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height: 0;
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border-color: transparent;
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border-style: solid;
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border-width: 5px 0 5px 5px;
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border-left-color: #cccccc;
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margin-top: 5px;
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margin-right: -10px;
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}
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.dropdown-submenu:hover>a:after {
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2022-01-13 18:59:03 +00:00
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border-left-color: #adb5bd;
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2019-10-31 19:06:09 +00:00
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}
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.dropdown-submenu.pull-left {
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float: none;
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}
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.dropdown-submenu.pull-left>.dropdown-menu {
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left: -100%;
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margin-left: 10px;
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border-radius: 6px 0 6px 6px;
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}
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</style>
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2022-01-13 18:59:03 +00:00
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<script type="text/javascript">
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2019-10-31 19:06:09 +00:00
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// manage active state of menu based on current page
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$(document).ready(function () {
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// active menu anchor
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href = window.location.pathname
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href = href.substr(href.lastIndexOf('/') + 1)
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if (href === "")
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href = "index.html";
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var menuAnchor = $('a[href="' + href + '"]');
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2023-02-08 20:04:22 +00:00
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// mark the anchor link active (and if it's in a dropdown, also mark that active)
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var dropdown = menuAnchor.closest('li.dropdown');
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if (window.bootstrap) { // Bootstrap 4+
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menuAnchor.addClass('active');
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dropdown.find('> .dropdown-toggle').addClass('active');
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} else { // Bootstrap 3
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menuAnchor.parent().addClass('active');
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dropdown.addClass('active');
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}
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2022-01-13 18:59:03 +00:00
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// Navbar adjustments
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var navHeight = $(".navbar").first().height() + 15;
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var style = document.createElement('style');
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var pt = "padding-top: " + navHeight + "px; ";
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var mt = "margin-top: -" + navHeight + "px; ";
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var css = "";
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// offset scroll position for anchor links (for fixed navbar)
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for (var i = 1; i <= 6; i++) {
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css += ".section h" + i + "{ " + pt + mt + "}\n";
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}
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style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
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document.head.appendChild(style);
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2019-10-31 19:06:09 +00:00
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});
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</script>
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<!-- tabsets -->
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<style type="text/css">
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.tabset-dropdown > .nav-tabs {
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display: inline-table;
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max-height: 500px;
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min-height: 44px;
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overflow-y: auto;
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border: 1px solid #ddd;
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border-radius: 4px;
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}
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2023-10-26 18:13:30 +00:00
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.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
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content: "\e259";
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2019-10-31 19:06:09 +00:00
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font-family: 'Glyphicons Halflings';
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display: inline-block;
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padding: 10px;
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border-right: 1px solid #ddd;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
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2023-10-26 18:13:30 +00:00
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content: "\e258";
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2019-10-31 19:06:09 +00:00
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font-family: 'Glyphicons Halflings';
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2023-10-26 18:13:30 +00:00
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border: none;
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2019-10-31 19:06:09 +00:00
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}
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.tabset-dropdown > .nav-tabs > li.active {
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display: block;
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}
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.tabset-dropdown > .nav-tabs > li > a,
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.tabset-dropdown > .nav-tabs > li > a:focus,
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.tabset-dropdown > .nav-tabs > li > a:hover {
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border: none;
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display: inline-block;
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border-radius: 4px;
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2020-04-27 20:35:41 +00:00
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background-color: transparent;
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2019-10-31 19:06:09 +00:00
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
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display: block;
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float: none;
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}
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.tabset-dropdown > .nav-tabs > li {
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display: none;
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}
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</style>
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<!-- code folding -->
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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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2020-04-27 20:35:41 +00:00
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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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2019-10-31 19:06:09 +00:00
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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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}
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@media (max-width: 767px) {
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div.tocify {
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width: 100%;
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max-width: none;
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}
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}
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.tocify ul, .tocify li {
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line-height: 20px;
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}
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.tocify-subheader .tocify-item {
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font-size: 0.90em;
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}
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Background
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CDM Versions
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CDM Proposals
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<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
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2019-10-31 19:06:09 +00:00
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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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<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
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How to
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<a href="download.html">Download the DDL</a>
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2021-09-22 19:39:44 +00:00
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<a href="cdmRPackage.html">Use the CDM R Package</a>
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<a href="drug_dose.html">Calculate Drug Dose</a>
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Support
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<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
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<a href="faq.html">FAQ</a>
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<a href="sqlScripts.html">SQL Scripts</a>
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<ul class="nav navbar-nav navbar-right">
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<a href="https://github.com/OHDSI/CommonDataModel">
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</div><!--/.nav-collapse -->
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</div><!--/.container -->
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</div><!--/.navbar -->
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2022-01-13 18:59:03 +00:00
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<div id="header">
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2023-02-08 20:04:22 +00:00
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<h1 class="title toc-ignore"><img src="ohdsi40x40.png"></img> OMOP CDM
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Background</h1>
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</div>
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<div id="background" class="section level2">
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<h2>Background</h2>
|
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<p>The Observational Medical Outcomes Partnership (OMOP) was a
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public-private partnership established to inform the appropriate use of
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observational healthcare databases for studying the effects of medical
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products. Over the course of the 5-year project and through its
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community of researchers from industry, government, and academia, OMOP
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successfully achieved its aims to:</p>
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<ul>
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<li>Conduct methodological research to empirically evaluate the
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performance of various analytical methods on their ability to identify
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true associations and avoid false findings</li>
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<li>Develop tools and capabilities for transforming, characterizing, and
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analysing disparate data sources across the health care delivery
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spectrum</li>
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<li>Establish a shared resource so that the broader research community
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can collaboratively advance the science</li>
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</ul>
|
2023-02-08 20:04:22 +00:00
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<p>The results of OMOP’s research has been widely published and
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presented at scientific conferences, including <a
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href="https://www.ohdsi.org/2021-ohdsi-global-symposium-info/">annual
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symposia</a>.</p>
|
2019-10-31 19:06:09 +00:00
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<p>The OMOP Legacy continues…</p>
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2023-02-08 20:04:22 +00:00
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<p>The community is actively using the OMOP Common Data Model for their
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various research purposes. Those tools will continue to be maintained
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and supported, and information about this work is available in the <a
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href="http://www.github.com/ohdsi">public domain</a>.</p>
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<p>The OMOP Common Data Model will continue to be an open-source
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community standard for observational healthcare data. The model
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specifications and associated work products will be placed in the public
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domain, and the entire research community is encouraged to use these
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tools to support everybody’s own research activities.</p>
|
2019-10-31 19:06:09 +00:00
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</div>
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<div id="the-role-of-the-common-data-model" class="section level2">
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<h2>The Role of the Common Data Model</h2>
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2023-02-08 20:04:22 +00:00
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<p>No single observational data source provides a comprehensive view of
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the clinical data a patient accumulates while receiving healthcare, and
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therefore none can be sufficient to meet all expected outcome analysis
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needs. This explains the need for assessing and analyzing multiple data
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sources concurrently using a common data standard. This standard is
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provided by the OMOP Common Data Model (CDM).</p>
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<p>The CDM is designed to support the conduct of research to identify
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and evaluate associations between interventions (drug exposure,
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procedures, healthcare policy changes etc.) and outcomes caused by these
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interventions (condition occurrences, procedures, drug exposure etc.).
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Outcomes can be efficacious (benefit) or adverse (safety risk). Often
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times, specific patient cohorts (e.g., those taking a certain drug or
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suffering from a certain disease) may be defined for treatments or
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outcomes, using clinical events (diagnoses, observations, procedures,
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etc.) that occur in predefined temporal relationships to each other. The
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CDM, combined with its standardized content (via the Standardized
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Vocabularies), will ensure that research methods can be systematically
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applied to produce meaningfully comparable and reproducible results.</p>
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2019-10-31 19:06:09 +00:00
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</div>
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<div id="design-principles" class="section level2">
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<h2>Design Principles</h2>
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2023-02-08 20:04:22 +00:00
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<p>The CDM is designed to include all observational health data elements
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(experiences of the patient receiving health care) that are relevant for
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analytic use cases to support the generation of reliable scientific
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evidence about disease natural history, healthcare delivery, effects of
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medical interventions, the identification of demographic information,
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health care interventions and outcomes.</p>
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<p>Therefore, the CDM is designed to store observational data to allow
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for research, under the following principles:</p>
|
2019-10-31 19:06:09 +00:00
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<ul>
|
2023-02-08 20:04:22 +00:00
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<li><strong>Suitability for purpose:</strong> The CDM aims to provide
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data organized in a way optimal for analysis, rather than for the
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purpose of addressing the operational needs of health care providers or
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payers.</li>
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<li><strong>Data protection:</strong> All data that might jeopardize the
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identity and protection of patients, such as names, precise birthdays
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etc. are limited. Exceptions are possible where the research expressly
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requires more detailed information, such as precise birth dates for the
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study of infants.</li>
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<li><strong>Design of domains:</strong> The domains are modeled in a
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person-centric relational data model, where for each record the identity
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of the person and a date is captured as a minimum.</li>
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<li><strong>Rationale for domains:</strong> Domains are identified and
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separately defined in an entity-relationship model if they have an
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analysis use case and the domain has specific attributes that are not
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otherwise applicable. All other data can be preserved as an observation
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in an entity-attribute-value structure.</li>
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<li><strong>Standardized Vocabularies:</strong> To standardize the
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content of those records, the CDM relies on the Standardized
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Vocabularies containing all necessary and appropriate corresponding
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standard healthcare concepts.</li>
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<li><strong>Reuse of existing vocabularies:</strong> If possible, these
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concepts are leveraged from national or industry standardization or
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vocabulary definition organizations or initiatives, such as the National
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Library of Medicine, the Department of Veterans’ Affairs, the Center of
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Disease Control and Prevention, etc.</li>
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<li><strong>Maintaining source codes:</strong> Even though all codes are
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mapped to the Standardized Vocabularies, the model also stores the
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original source code to ensure no information is lost.</li>
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<li><strong>Technology neutrality:</strong> The CDM does not require a
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specific technology. It can be realized in any relational database, such
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as Oracle, SQL Server etc., or as SAS analytical datasets.</li>
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<li><strong>Scalability:</strong> The CDM is optimized for data
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processing and computational analysis to accommodate data sources that
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vary in size, including databases with up to hundreds of millions of
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persons and billions of clinical observations.</li>
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<li><strong>Backwards compatibility:</strong> All changes from previous
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CDMs are clearly delineated in the <a
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href="https://github.com/OHDSI/CommonDataModel">github repository</a>.
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Older versions of the CDM can be easily created from the CDMv5, and no
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information is lost that was present previously.</li>
|
2019-10-31 19:06:09 +00:00
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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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<script>
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// add bootstrap table styles to pandoc tables
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function bootstrapStylePandocTables() {
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2021-01-06 15:52:57 +00:00
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$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
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2019-10-31 19:06:09 +00:00
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}
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$(document).ready(function () {
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bootstrapStylePandocTables();
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});
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</script>
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2020-04-27 20:35:41 +00:00
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<!-- tabsets -->
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<script>
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$(document).ready(function () {
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window.buildTabsets("TOC");
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});
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$(document).ready(function () {
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$('.tabset-dropdown > .nav-tabs > li').click(function () {
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2022-01-13 18:59:03 +00:00
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$(this).parent().toggleClass('nav-tabs-open');
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2020-04-27 20:35:41 +00:00
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});
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});
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</script>
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<!-- code folding -->
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<script>
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$(document).ready(function () {
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2022-01-13 18:59:03 +00:00
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// temporarily add toc-ignore selector to headers for the consistency with Pandoc
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$('.unlisted.unnumbered').addClass('toc-ignore')
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2020-04-27 20:35:41 +00:00
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// move toc-ignore selectors from section div to header
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$('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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selectors: "h1,h2,h3",
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theme: "bootstrap3",
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context: '.toc-content',
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hashGenerator: function (text) {
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return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
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2020-04-27 20:35:41 +00:00
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},
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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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2019-10-31 19:06:09 +00:00
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