2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +00:00
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2021-09-23 14:52:05 +00:00
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<title>OMOP CDM v6.0</title>
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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2022-04-07 15:14:50 +00:00
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2019-08-28 15:02:47 +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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2022-04-07 15:14:50 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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2019-08-28 15:02:47 +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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CDM Versions
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CDM 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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How to
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<a href="download.html">Download the DDL</a>
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2020-10-06 15:11:13 +00:00
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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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2020-10-06 15:11:13 +00:00
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2022-07-27 01:48:28 +00:00
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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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2019-08-28 15:02:47 +00:00
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2019-10-31 19:06:09 +00:00
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2019-08-28 15:02:47 +00:00
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</div><!--/.container -->
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2022-01-13 18:59:03 +00:00
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2021-09-23 14:52:05 +00:00
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<h1 class="title toc-ignore"><strong>OMOP CDM v6.0</strong></h1>
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2019-08-28 15:02:47 +00:00
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</div>
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2021-06-03 14:45:05 +00:00
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<div id="note-about-cdm-v6.0" class="section level2">
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<h2>NOTE ABOUT CDM v6.0</h2>
|
2023-02-08 20:04:22 +00:00
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<p>Please be aware that v6.0 of the OMOP CDM is <strong>not</strong>
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fully supported by the OHDSI suite of tools and methods. The major
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difference in CDM v5.3 and CDM v6.0 involves switching the *_datetime
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fields to mandatory rather than optional. This switch radically changes
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the assumptions related to exposure and outcome timing. Rather than move
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forward with v6.0, CDM v5.4 was designed with additions to the model
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that have been requested by the community while retaining the date
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structure of medical events in v5.3. Please see our the specifications
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for <a href="http://ohdsi.github.io/CommonDataModel/cdm54.html">CDM
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v5.4</a> and detailed <a
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href="http://ohdsi.github.io/CommonDataModel/cdm54Changes.html">changes
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from CDM v5.3</a>. <strong>For new collaborators to OHDSI, please
|
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|
transform your data to <a
|
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|
|
href="https://github.com/OHDSI/CommonDataModel/releases/tag/v5.4.0">CDM
|
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v5.4</a> until such time that the v6 series of the CDM is ready for
|
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mainstream use.</strong></p>
|
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|
<p>Below is the specification document for the OMOP Common Data Model,
|
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|
|
|
|
v6.0. Each table is represented with a high-level description and ETL
|
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conventions that should be followed. This is continued with a discussion
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of each field in each table, any conventions related to the field, and
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constraints that should be followed (like primary key, foreign key,
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etc). Should you have questions please feel free to visit the <a
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|
href="https://forums.ohdsi.org/">forums</a> or the <a
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href="https://github.com/ohdsi/CommonDataModel/issues">github issue</a>
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page.</p>
|
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<p>–after regeneration of DDLs link to csv of cdm link to pdf of cdm
|
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documentation link to forum on doc page</p>
|
2021-06-03 14:45:05 +00:00
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</div>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<div id="changes-in-v6.0" class="section level2">
|
|
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|
<h2><strong>Changes in v6.0</strong></h2>
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<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Latitude and Longitude added to <a
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|
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href="https://ohdsi.github.io/CommonDataModel/cdm60.html#location">LOCATION</a></li>
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|
<li>Contract owner field added to <a
|
|
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|
|
href="https://ohdsi.github.io/CommonDataModel/cdm60.html#payer_plan_period">PAYER_PLAN_PERIOD</a></li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<li>All primary keys were changed to bigint</li>
|
2023-02-08 20:04:22 +00:00
|
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|
|
<li>The name of ADMISSION_SOURCE_CONCEPT_ID was changed to
|
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|
|
ADMITTED_FROM_CONCEPT_ID in <a
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href="https://ohdsi.github.io/CommonDataModel/cdm60.html#visit_occurrence">VISIT_OCCURRENCE</a>
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and <a
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href="https://ohdsi.github.io/CommonDataModel/cdm60.html#visit_detail">VISIT_DETAIL</a></li>
|
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|
<li>All Concept_Ids are now mandatory except for UNIT_CONCEPT_ID,
|
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VALUE_AS_CONCEPT_ID, and OPERATOR_CONCEPT_ID. If there is no value
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|
|
available then a Concept_Id should be set to 0 instead of NULL.</li>
|
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|
<li><a
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|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#death">DEATH</a>
|
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table removed and DEATH_DATETIME field added to the <a
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href="https://ohdsi.github.io/CommonDataModel/cdm60.html#person">PERSON</a>
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table. Cause of death is stored in the <a
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href="https://ohdsi.github.io/CommonDataModel/cdm60.html#condition_occurrence">CONDITION_OCCURRENCE</a></li>
|
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|
|
<li>DATETIME fields were made mandatory and date fields were made
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optional.</li>
|
2020-10-06 15:11:13 +00:00
|
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</ul>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
<div id="person" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
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|
<h3 class="tabset tabset-pills">person</h3>
|
2020-10-06 15:11:13 +00:00
|
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|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
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<p>This table serves as the central identity management for all Persons
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in the database. It contains records that uniquely identify each person
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or patient, and some demographic information.</p>
|
2020-10-06 15:11:13 +00:00
|
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|
<p><strong>User Guide</strong></p>
|
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|
<p>All records in this table are independent Persons.</p>
|
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|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
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|
<p>All Persons in a database needs one record in this table, unless they
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fail data quality requirements specified in the ETL. Persons with no
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|
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Events should have a record nonetheless. If more than one data source
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contributes Events to the database, Persons must be reconciled, if
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|
possible, across the sources to create one single record per Person. The
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BIRTH_DATETIME must be equivalent to the content of BIRTH_DAY,
|
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|
BIRTH_MONTH and BIRTH_YEAR. There is a helpful rule listed in table
|
|
|
|
|
|
below for how to derive BIRTH_DATETIME if it is not available in the
|
|
|
|
|
|
source. <strong>New to CDM v6.0</strong> The person’s death date is now
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|
|
stored in this table instead of the separate DEATH table. In the case
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|
|
that multiple dates of death are given in the source data the ETL should
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|
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|
make a choice as to which death date to put in the PERSON table. Any
|
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|
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additional dates can be stored in the OBSERVATION table using the
|
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|
concept <a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/4265167">4265167</a>
|
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which stands for ‘Date of death’ . Similarly, the cause of death is
|
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|
stored in the CONDITION_OCCURRENCE table using the
|
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|
|
CONDITION_STATUS_CONCEPT_ID <a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/32891">32891</a> for
|
|
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|
|
‘Cause of death’.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="observation_period" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">observation_period</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>This table contains records which define spans of time during which
|
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|
|
|
|
two conditions are expected to hold: (i) Clinical Events that happened
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|
|
to the Person are recorded in the Event tables, and (ii) absense of
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|
|
|
records indicate such Events did not occur during this span of time.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>For each Person, one or more OBSERVATION_PERIOD records may be
|
|
|
|
|
|
present, but they will not overlap or be back to back to each other.
|
|
|
|
|
|
Events may exist outside all of the time spans of the OBSERVATION_PERIOD
|
|
|
|
|
|
records for a patient, however, absence of an Event outside these time
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|
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|
|
|
spans cannot be construed as evidence of absence of an Event. Incidence
|
|
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|
|
|
or prevalence rates should only be calculated for the time of active
|
|
|
|
|
|
OBSERVATION_PERIOD records. When constructing cohorts, outside Events
|
|
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|
|
can be used for inclusion criteria definition, but without any guarantee
|
|
|
|
|
|
for the performance of these criteria. Also, OBSERVATION_PERIOD records
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|
|
|
|
|
can be as short as a single day, greatly disturbing the denominator of
|
|
|
|
|
|
any rate calculation as part of cohort characterizations. To avoid that,
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|
|
|
|
|
apply minimal observation time as a requirement for any cohort
|
|
|
|
|
|
definition.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Each Person needs to have at least one OBSERVATION_PERIOD record,
|
|
|
|
|
|
which should represent time intervals with a high capture rate of
|
|
|
|
|
|
Clinical Events. Some source data have very similar concepts, such as
|
|
|
|
|
|
enrollment periods in insurance claims data. In other source data such
|
|
|
|
|
|
as most EHR systems these time spans need to be inferred under a set of
|
|
|
|
|
|
assumptions. It is the discretion of the ETL developer to define these
|
|
|
|
|
|
assumptions. In many ETL solutions the start date of the first
|
|
|
|
|
|
occurrence or the first high quality occurrence of a Clinical Event
|
|
|
|
|
|
(Condition, Drug, Procedure, Device, Measurement, Visit) is defined as
|
|
|
|
|
|
the start of the OBSERVATION_PERIOD record, and the end date of the last
|
|
|
|
|
|
occurrence of last high quality occurrence of a Clinical Event, or the
|
|
|
|
|
|
end of the database period becomes the end of the OBSERVATOIN_PERIOD for
|
|
|
|
|
|
each Person. If a Person only has a single Clinical Event the
|
|
|
|
|
|
OBSERVATION_PERIOD record can be as short as one day. Depending on these
|
|
|
|
|
|
definitions it is possible that Clinical Events fall outside the time
|
|
|
|
|
|
spans defined by OBSERVATION_PERIOD records. Family history or history
|
|
|
|
|
|
of Clinical Events generally are not used to generate OBSERVATION_PERIOD
|
|
|
|
|
|
records around the time they are referring to. Any two overlapping or
|
|
|
|
|
|
adjacent OBSERVATION_PERIOD records have to be merged into one.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="visit_occurrence" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">visit_occurrence</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>This table contains Events where Persons engage with the healthcare
|
|
|
|
|
|
system for a duration of time. They are often also called “Encounters”.
|
|
|
|
|
|
Visits are defined by a configuration of circumstances under which they
|
|
|
|
|
|
occur, such as (i) whether the patient comes to a healthcare
|
|
|
|
|
|
institution, the other way around, or the interaction is remote, (ii)
|
|
|
|
|
|
whether and what kind of trained medical staff is delivering the service
|
|
|
|
|
|
during the Visit, and (iii) whether the Visit is transient or for a
|
|
|
|
|
|
longer period involving a stay in bed.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The configuration defining the Visit are described by Concepts in the
|
|
|
|
|
|
Visit Domain, which form a hierarchical structure, but rolling up to
|
|
|
|
|
|
generally familiar Visits adopted in most healthcare systems
|
|
|
|
|
|
worldwide:</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li><a href="https://athena.ohdsi.org/search-terms/terms/9201">Inpatient
|
|
|
|
|
|
Visit</a>: Person visiting hospital, at a Care Site, in bed, for
|
|
|
|
|
|
duration of more than one day, with physicians and other Providers
|
|
|
|
|
|
permanently available to deliver service around the clock</li>
|
|
|
|
|
|
<li><a href="https://athena.ohdsi.org/search-terms/terms/9203">Emergency
|
|
|
|
|
|
Room Visit</a>: Person visiting dedicated healthcare institution for
|
|
|
|
|
|
treating emergencies, at a Care Site, within one day, with physicians
|
|
|
|
|
|
and Providers permanently available to deliver service around the
|
|
|
|
|
|
clock</li>
|
|
|
|
|
|
<li><a href="https://athena.ohdsi.org/search-terms/terms/262">Emergency
|
|
|
|
|
|
Room and Inpatient Visit</a>: Person visiting ER followed by a
|
|
|
|
|
|
subsequent Inpatient Visit, where Emergency department is part of
|
|
|
|
|
|
hospital, and transition from the ER to other hospital departments is
|
|
|
|
|
|
undefined</li>
|
|
|
|
|
|
<li><a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/42898160">Non-hospital
|
|
|
|
|
|
institution Visit</a>: Person visiting dedicated institution for reasons
|
|
|
|
|
|
of poor health, at a Care Site, long-term or permanently, with no
|
|
|
|
|
|
physician but possibly other Providers permanently available to deliver
|
|
|
|
|
|
service around the clock</li>
|
|
|
|
|
|
<li><a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/9202">Outpatient
|
|
|
|
|
|
Visit</a>: Person visiting dedicated ambulatory healthcare institution,
|
|
|
|
|
|
at a Care Site, within one day, without bed, with physicians or medical
|
|
|
|
|
|
Providers delivering service during Visit</li>
|
|
|
|
|
|
<li><a href="https://athena.ohdsi.org/search-terms/terms/581476">Home
|
|
|
|
|
|
Visit</a>: Provider visiting Person, without a Care Site, within one
|
|
|
|
|
|
day, delivering service</li>
|
|
|
|
|
|
<li><a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/5083">Telehealth
|
|
|
|
|
|
Visit</a>: Patient engages with Provider through communication
|
|
|
|
|
|
media</li>
|
|
|
|
|
|
<li><a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/581458">Pharmacy
|
|
|
|
|
|
Visit</a>: Person visiting pharmacy for dispensing of Drug, at a Care
|
|
|
|
|
|
Site, within one day</li>
|
|
|
|
|
|
<li><a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/32036">Laboratory
|
|
|
|
|
|
Visit</a>: Patient visiting dedicated institution, at a Care Site,
|
|
|
|
|
|
within one day, for the purpose of a Measurement.</li>
|
|
|
|
|
|
<li><a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/581478">Ambulance
|
|
|
|
|
|
Visit</a>: Person using transportation service for the purpose of
|
|
|
|
|
|
initiating one of the other Visits, without a Care Site, within one day,
|
|
|
|
|
|
potentially with Providers accompanying the Visit and delivering
|
|
|
|
|
|
service</li>
|
|
|
|
|
|
<li><a href="https://athena.ohdsi.org/search-terms/terms/38004193">Case
|
|
|
|
|
|
Management Visit</a>: Person interacting with healthcare system, without
|
|
|
|
|
|
a Care Site, within a day, with no Providers involved, for
|
|
|
|
|
|
administrative purposes</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The Visit duration, or ‘length of stay’, is defined as VISIT_END_DATE
|
|
|
|
|
|
- VISIT_START_DATE. For all Visits this is <1 day, except Inpatient
|
|
|
|
|
|
Visits and Non-hospital institution Visits. The CDM also contains the
|
|
|
|
|
|
VISIT_DETAIL table where additional information about the Visit is
|
|
|
|
|
|
stored, for example, transfers between units during an inpatient
|
|
|
|
|
|
Visit.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Visits can be derived easily if the source data contain coding
|
|
|
|
|
|
systems for Place of Service or Procedures, like CPT codes for well
|
|
|
|
|
|
visits. In those cases, the codes can be looked up and mapped to a
|
|
|
|
|
|
Standard Visit Concept. Otherwise, Visit Concepts have to be identified
|
|
|
|
|
|
in the ETL process. This table will contain concepts in the Visit
|
|
|
|
|
|
domain. These concepts are arranged in a hierarchical structure to
|
|
|
|
|
|
facilitate cohort definitions by rolling up to generally familiar Visits
|
|
|
|
|
|
adopted in most healthcare systems worldwide. Visits can be adjacent to
|
|
|
|
|
|
each other, i.e. the end date of one can be identical with the start
|
|
|
|
|
|
date of the other. As a consequence, more than one-day Visits or their
|
|
|
|
|
|
descendants can be recorded for the same day. Multi-day visits must not
|
|
|
|
|
|
overlap, i.e. share days other than start and end days. It is often the
|
|
|
|
|
|
case that some logic should be written for how to define visits and how
|
|
|
|
|
|
to assign Visit_Concept_Id. For example, in US claims outpatient visits
|
|
|
|
|
|
that appear to occur within the time period of an inpatient visit can be
|
|
|
|
|
|
rolled into one with the same Visit_Occurrence_Id. In EHR data inpatient
|
|
|
|
|
|
visits that are within one day of each other may be strung together to
|
|
|
|
|
|
create one visit. It will all depend on the source data and how
|
|
|
|
|
|
encounter records should be translated to visit occurrences. Providers
|
|
|
|
|
|
can be associated with a Visit through the PROVIDER_ID field, or
|
|
|
|
|
|
indirectly through PROCEDURE_OCCURRENCE records linked both to the VISIT
|
|
|
|
|
|
and PROVIDER tables.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="visit_detail" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">visit_detail</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The VISIT_DETAIL table is an optional table used to represents
|
|
|
|
|
|
details of each record in the parent VISIT_OCCURRENCE table. A good
|
|
|
|
|
|
example of this would be the movement between units in a hospital during
|
|
|
|
|
|
an inpatient stay or claim lines associated with a one insurance claim.
|
|
|
|
|
|
For every record in the VISIT_OCCURRENCE table there may be 0 or more
|
|
|
|
|
|
records in the VISIT_DETAIL table with a 1:n relationship where n may be
|
|
|
|
|
|
0. The VISIT_DETAIL table is structurally very similar to
|
|
|
|
|
|
VISIT_OCCURRENCE table and belongs to the visit domain.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The configuration defining the Visit Detail is described by Concepts
|
|
|
|
|
|
in the Visit Domain, which form a hierarchical structure. The Visit
|
|
|
|
|
|
Detail record will have an associated to the Visit Occurrence record in
|
|
|
|
|
|
two ways: <br> 1. The Visit Detail record will have the
|
|
|
|
|
|
VISIT_OCCURRENCE_ID it is associated to 2. The VISIT_DETAIL_CONCEPT_ID
|
|
|
|
|
|
will be a descendant of the VISIT_CONCEPT_ID for the Visit.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>It is not mandatory that the VISIT_DETAIL table be filled in, but if
|
|
|
|
|
|
you find that the logic to create VISIT_OCCURRENCE records includes the
|
|
|
|
|
|
roll-up of multiple smaller records to create one picture of a Visit
|
|
|
|
|
|
then it is a good idea to use VISIT_DETAIL. In EHR data, for example, a
|
|
|
|
|
|
Person may be in the hospital but instead of one over-arching Visit
|
|
|
|
|
|
their encounters are recorded as times they interacted with a health
|
|
|
|
|
|
care provider. A Person in the hospital interacts with multiple
|
|
|
|
|
|
providers multiple times a day so the encounters must be strung together
|
|
|
|
|
|
using some heuristic (defined by the ETL) to identify the entire Visit.
|
|
|
|
|
|
In this case the encounters would be considered Visit Details and the
|
|
|
|
|
|
entire Visit would be the Visit Occurrence. In this example it is also
|
|
|
|
|
|
possible to use the Vocabulary to distinguish Visit Details from a Visit
|
|
|
|
|
|
Occurrence by setting the VISIT_CONCEPT_ID to <a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/9201">9201</a> and the
|
|
|
|
|
|
VISIT_DETAIL_CONCEPT_IDs either to 9201 or its children to indicate
|
|
|
|
|
|
where the patient was in the hospital at the time of care.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<div id="condition_occurrence"
|
|
|
|
|
|
class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">condition_occurrence</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>This table contains records of Events of a Person suggesting the
|
|
|
|
|
|
presence of a disease or medical condition stated as a diagnosis, a
|
|
|
|
|
|
sign, or a symptom, which is either observed by a Provider or reported
|
|
|
|
|
|
by the patient.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Conditions are defined by Concepts from the Condition domain, which
|
|
|
|
|
|
form a complex hierarchy. As a result, the same Person with the same
|
|
|
|
|
|
disease may have multiple Condition records, which belong to the same
|
|
|
|
|
|
hierarchical family. Most Condition records are mapped from diagnostic
|
|
|
|
|
|
codes, but recorded signs, symptoms and summary descriptions also
|
|
|
|
|
|
contribute to this table. Rule out diagnoses should not be recorded in
|
|
|
|
|
|
this table, but in reality their negating nature is not always captured
|
|
|
|
|
|
in the source data, and other precautions must be taken when when
|
|
|
|
|
|
identifying Persons who should suffer from the recorded Condition.
|
|
|
|
|
|
Record all conditions as they exist in the source data. Any decisions
|
|
|
|
|
|
about diagnosis/phenotype definitions would be done through cohort
|
|
|
|
|
|
specifications. These cohorts can be housed in the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#payer_plan_period">COHORT</a>
|
|
|
|
|
|
table. Conditions span a time interval from start to end, but are
|
|
|
|
|
|
typically recorded as single snapshot records with no end date. The
|
|
|
|
|
|
reason is twofold: (i) At the time of the recording the duration is not
|
|
|
|
|
|
known and later not recorded, and (ii) the Persons typically cease
|
|
|
|
|
|
interacting with the healthcare system when they feel better, which
|
|
|
|
|
|
leads to incomplete capture of resolved Conditions. The <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#condition_era">CONDITION_ERA</a>
|
|
|
|
|
|
table addresses this issue. Family history and past diagnoses (‘history
|
|
|
|
|
|
of’) are not recorded in this table. Instead, they are listed in the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
|
|
|
|
|
|
table. Codes written in the process of establishing the diagnosis, such
|
|
|
|
|
|
as ‘question of’ of and ‘rule out’, should not represented here.
|
|
|
|
|
|
Instead, they should be recorded in the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
|
|
|
|
|
|
table, if they are used for analyses. However, this information is not
|
|
|
|
|
|
always available.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Source codes and source text fields mapped to Standard Concepts of
|
|
|
|
|
|
the Condition Domain have to be recorded here.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="drug_exposure" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">drug_exposure</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>This table captures records about the exposure to a Drug ingested or
|
|
|
|
|
|
otherwise introduced into the body. A Drug is a biochemical substance
|
|
|
|
|
|
formulated in such a way that when administered to a Person it will
|
|
|
|
|
|
exert a certain biochemical effect on the metabolism. Drugs include
|
|
|
|
|
|
prescription and over-the-counter medicines, vaccines, and
|
|
|
|
|
|
large-molecule biologic therapies. Radiological devices ingested or
|
|
|
|
|
|
applied locally do not count as Drugs.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The purpose of records in this table is to indicate an exposure to a
|
|
|
|
|
|
certain drug as best as possible. In this context a drug is defined as
|
|
|
|
|
|
an active ingredient. Drug Exposures are defined by Concepts from the
|
|
|
|
|
|
Drug domain, which form a complex hierarchy. As a result, one
|
|
|
|
|
|
DRUG_SOURCE_CONCEPT_ID may map to multiple standard concept ids if it is
|
|
|
|
|
|
a combination product. Records in this table represent prescriptions
|
|
|
|
|
|
written, prescriptions dispensed, and drugs administered by a provider
|
|
|
|
|
|
to name a few. The DRUG_TYPE_CONCEPT_ID can be used to find and filter
|
|
|
|
|
|
on these types. This table includes additional information about the
|
|
|
|
|
|
drug products, the quantity given, and route of administration.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Information about quantity and dose is provided in a variety of
|
|
|
|
|
|
different ways and it is important for the ETL to provide as much
|
|
|
|
|
|
information as possible from the data. Depending on the provenance of
|
|
|
|
|
|
the data fields may be captured differently i.e. quantity for drugs
|
|
|
|
|
|
administered may have a separate meaning from quantity for prescriptions
|
|
|
|
|
|
dispensed. If a patient has multiple records on the same day for the
|
|
|
|
|
|
same drug or procedures the ETL should not de-dupe them unless there is
|
|
|
|
|
|
probable reason to believe the item is a true data duplicate. Take note
|
|
|
|
|
|
on how to handle refills for prescriptions written.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<div id="procedure_occurrence"
|
|
|
|
|
|
class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">procedure_occurrence</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>This table contains records of activities or processes ordered by, or
|
|
|
|
|
|
carried out by, a healthcare provider on the patient with a diagnostic
|
|
|
|
|
|
or therapeutic purpose.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Lab tests are not a procedure, if something is observed with an
|
|
|
|
|
|
expected resulting amount and unit then it should be a measurement.
|
|
|
|
|
|
Phlebotomy is a procedure but so trivial that it tends to be rarely
|
|
|
|
|
|
captured. It can be assumed that there is a phlebotomy procedure
|
|
|
|
|
|
associated with many lab tests, therefore it is unnecessary to add them
|
|
|
|
|
|
as separate procedures. If the user finds the same procedure over
|
|
|
|
|
|
concurrent days, it is assumed those records are part of a procedure
|
|
|
|
|
|
lasting more than a day. This logic is in lieu of the
|
|
|
|
|
|
procedure_end_date, which will be added in a future version of the
|
|
|
|
|
|
CDM.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>If a procedure lasts more than a day, then it should be recorded as a
|
|
|
|
|
|
separate record for each day the procedure occurred, this logic is in
|
|
|
|
|
|
lieu of the PROCEDURE_END_DATE, which will be added in a future version
|
|
|
|
|
|
of the CDM. When dealing with duplicate records, the ETL must determine
|
|
|
|
|
|
whether to sum them up into one record or keep them separate. Things to
|
|
|
|
|
|
consider are: - Same Procedure - Same PROCEDURE_DATETIME - Same Visit
|
|
|
|
|
|
Occurrence or Visit Detail - Same Provider - Same Modifier for
|
|
|
|
|
|
Procedures. Source codes and source text fields mapped to Standard
|
|
|
|
|
|
Concepts of the Procedure Domain have to be recorded here.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="device_exposure" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">device_exposure</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The Device domain captures information about a person’s exposure to a
|
|
|
|
|
|
foreign physical object or instrument which is used for diagnostic or
|
|
|
|
|
|
therapeutic purposes through a mechanism beyond chemical action. Devices
|
|
|
|
|
|
include implantable objects (e.g. pacemakers, stents, artificial
|
|
|
|
|
|
joints), medical equipment and supplies (e.g. bandages, crutches,
|
|
|
|
|
|
syringes), other instruments used in medical procedures (e.g. sutures,
|
|
|
|
|
|
defibrillators) and material used in clinical care (e.g. adhesives, body
|
|
|
|
|
|
material, dental material, surgical material).</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The distinction between Devices or supplies and Procedures are
|
|
|
|
|
|
sometimes blurry, but the former are physical objects while the latter
|
|
|
|
|
|
are actions, often to apply a Device or supply.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Source codes and source text fields mapped to Standard Concepts of
|
|
|
|
|
|
the Device Domain have to be recorded here.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="measurement" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">measurement</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The MEASUREMENT table contains records of Measurements,
|
|
|
|
|
|
i.e. structured values (numerical or categorical) obtained through
|
|
|
|
|
|
systematic and standardized examination or testing of a Person or
|
|
|
|
|
|
Person’s sample. The MEASUREMENT table contains both orders and results
|
|
|
|
|
|
of such Measurements as laboratory tests, vital signs, quantitative
|
|
|
|
|
|
findings from pathology reports, etc. Measurements are stored as
|
|
|
|
|
|
attribute value pairs, with the attribute as the Measurement Concept and
|
|
|
|
|
|
the value representing the result. The value can be a Concept (stored in
|
|
|
|
|
|
VALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with a Unit
|
|
|
|
|
|
(UNIT_CONCEPT_ID). The Procedure for obtaining the sample is housed in
|
|
|
|
|
|
the PROCEDURE_OCCURRENCE table, though it is unnecessary to create a
|
|
|
|
|
|
PROCEDURE_OCCURRENCE record for each measurement if one does not exist
|
|
|
|
|
|
in the source data. Measurements differ from Observations in that they
|
|
|
|
|
|
require a standardized test or some other activity to generate a
|
|
|
|
|
|
quantitative or qualitative result. If there is no result, it is assumed
|
|
|
|
|
|
that the lab test was conducted but the result was not captured.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Measurements are predominately lab tests with a few exceptions, like
|
|
|
|
|
|
blood pressure or function tests. Results are given in the form of a
|
|
|
|
|
|
value and unit combination. When investigating measurements, look for
|
|
|
|
|
|
operator_concept_ids (<, >, etc.).</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Only records where the source value maps to a Concept in the
|
|
|
|
|
|
measurement domain should be included in this table. Even though each
|
|
|
|
|
|
Measurement always has a result, the fields VALUE_AS_NUMBER and
|
|
|
|
|
|
VALUE_AS_CONCEPT_ID are not mandatory as often the result is not given
|
|
|
|
|
|
in the source data. When the result is not known, the Measurement record
|
|
|
|
|
|
represents just the fact that the corresponding Measurement was carried
|
|
|
|
|
|
out, which in itself is already useful information for some use cases.
|
|
|
|
|
|
For some Measurement Concepts, the result is included in the test. For
|
|
|
|
|
|
example, ICD10 CONCEPT_ID <a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/45548980">45548980</a>
|
|
|
|
|
|
‘Abnormal level of unspecified serum enzyme’ indicates a Measurement and
|
|
|
|
|
|
the result (abnormal). In those situations, the CONCEPT_RELATIONSHIP
|
|
|
|
|
|
table in addition to the ‘Maps to’ record contains a second record with
|
|
|
|
|
|
the relationship_id set to ‘Maps to value’. In this example, the ‘Maps
|
|
|
|
|
|
to’ relationship directs to <a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/4046263">4046263</a>
|
|
|
|
|
|
‘Enzyme measurement’ as well as a ‘Maps to value’ record to <a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/4135493">4135493</a>
|
|
|
|
|
|
‘Abnormal’.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="observation" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">observation</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The OBSERVATION table captures clinical facts about a Person obtained
|
|
|
|
|
|
in the context of examination, questioning or a procedure. Any data that
|
|
|
|
|
|
cannot be represented by any other domains, such as social and lifestyle
|
|
|
|
|
|
facts, medical history, family history, etc. are recorded here.
|
|
|
|
|
|
<strong>New to CDM v6.0</strong> An Observation can now be linked to
|
|
|
|
|
|
other records in the CDM instance using the fields OBSERVATION_EVENT_ID
|
|
|
|
|
|
and OBS_EVENT_FIELD_CONCEPT_ID. To link another record to an
|
|
|
|
|
|
Observation, the primary key goes in OBSERVATION_EVENT_ID
|
|
|
|
|
|
(CONDITION_OCCURRENCE_ID, DRUG_EXPOSURE_ID, etc.) and the Concept
|
|
|
|
|
|
representing the field where the OBSERVATION_EVENT_ID was taken from go
|
|
|
|
|
|
in the OBS_EVENT_FIELD_CONCEPT_ID. For example, a CONDITION_OCCURRENCE
|
|
|
|
|
|
of Asthma might be linked to an Observation of a family history of
|
|
|
|
|
|
Asthma. In this case the CONDITION_OCCURRENCE_ID of the Asthma record
|
|
|
|
|
|
would go in OBSERVATION_EVENT_ID of the family history record and the
|
|
|
|
|
|
CONCEPT_ID <a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms/1147127">1147127</a>
|
|
|
|
|
|
would go in OBS_EVENT_FIELD_CONCEPT_ID to denote that the
|
|
|
|
|
|
OBSERVATION_EVENT_ID represents a CONDITION_OCCURRENCE_ID.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Observations differ from Measurements in that they do not require a
|
|
|
|
|
|
standardized test or some other activity to generate clinical fact.
|
|
|
|
|
|
Typical observations are medical history, family history, the stated
|
|
|
|
|
|
need for certain treatment, social circumstances, lifestyle choices,
|
|
|
|
|
|
healthcare utilization patterns, etc. If the generation clinical facts
|
|
|
|
|
|
requires a standardized testing such as lab testing or imaging and leads
|
|
|
|
|
|
to a standardized result, the data item is recorded in the MEASUREMENT
|
|
|
|
|
|
table. If the clinical fact observed determines a sign, symptom,
|
|
|
|
|
|
diagnosis of a disease or other medical condition, it is recorded in the
|
|
|
|
|
|
CONDITION_OCCURRENCE table. Valid Observation Concepts are not enforced
|
|
|
|
|
|
to be from any domain though they still should be Standard Concepts.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Records whose Source Values map to any domain besides Condition,
|
|
|
|
|
|
Procedure, Drug, Measurement or Device should be stored in the
|
|
|
|
|
|
Observation table. Observations can be stored as attribute value pairs,
|
|
|
|
|
|
with the attribute as the Observation Concept and the value representing
|
|
|
|
|
|
the clinical fact. This fact can be a Concept (stored in
|
|
|
|
|
|
VALUE_AS_CONCEPT), a numerical value (VALUE_AS_NUMBER), a verbatim
|
|
|
|
|
|
string (VALUE_AS_STRING), or a datetime (VALUE_AS_DATETIME). Even though
|
|
|
|
|
|
Observations do not have an explicit result, the clinical fact can be
|
|
|
|
|
|
stated separately from the type of Observation in the VALUE_AS_* fields.
|
|
|
|
|
|
It is recommended for Observations that are suggestive statements of
|
|
|
|
|
|
positive assertion should have a value of ‘Yes’ (concept_id=4188539),
|
|
|
|
|
|
recorded, even though the null value is the equivalent.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="note" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">note</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The NOTE table captures unstructured information that was recorded by
|
|
|
|
|
|
a provider about a patient in free text (in ASCII, or preferably in UTF8
|
|
|
|
|
|
format) notes on a given date. The type of note_text is CLOB or
|
|
|
|
|
|
varchar(MAX) depending on RDBMS.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>HL7/LOINC CDO is a standard for consistent naming of documents to
|
|
|
|
|
|
support a range of use cases: retrieval, organization, display, and
|
|
|
|
|
|
exchange. It guides the creation of LOINC codes for clinical notes. CDO
|
|
|
|
|
|
annotates each document with 5 dimensions:</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li><strong>Kind of Document</strong>: Characterizes the general
|
|
|
|
|
|
structure of the document at a macro level (e.g. Anesthesia
|
|
|
|
|
|
Consent)</li>
|
|
|
|
|
|
<li><strong>Type of Service</strong>: Characterizes the kind of service
|
|
|
|
|
|
or activity (e.g. evaluations, consultations, and summaries). The notion
|
|
|
|
|
|
of time sequence, e.g., at the beginning (admission) at the end
|
|
|
|
|
|
(discharge) is subsumed in this axis. Example: Discharge Teaching.</li>
|
|
|
|
|
|
<li><strong>Setting</strong>: Setting is an extension of CMS’s
|
|
|
|
|
|
definitions (e.g. Inpatient, Outpatient)</li>
|
|
|
|
|
|
<li><strong>Subject Matter Domain (SMD)</strong>: Characterizes the
|
|
|
|
|
|
subject matter domain of a note (e.g. Anesthesiology)</li>
|
|
|
|
|
|
<li><strong>Role</strong>: Characterizes the training or professional
|
|
|
|
|
|
level of the author of the document, but does not break down to
|
|
|
|
|
|
specialty or subspecialty (e.g. Physician) Each combination of these 5
|
|
|
|
|
|
dimensions rolls up to a unique LOINC code.</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>According to CDO requirements, only 2 of the 5 dimensions are
|
|
|
|
|
|
required to properly annotate a document; Kind of Document and any one
|
|
|
|
|
|
of the other 4 dimensions. However, not all the permutations of the CDO
|
|
|
|
|
|
dimensions will necessarily yield an existing LOINC code. Each of these
|
|
|
|
|
|
dimensions are contained in the OMOP Vocabulary under the domain of
|
|
|
|
|
|
‘Meas Value’ with each dimension represented as a Concept Class.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="note_nlp" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">note_nlp</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The NOTE_NLP table encodes all output of NLP on clinical notes. Each
|
|
|
|
|
|
row represents a single extracted term from a note.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="specimen" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">specimen</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The specimen domain contains the records identifying biological
|
|
|
|
|
|
samples from a person.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Anatomic site is coded at the most specific level of granularity
|
|
|
|
|
|
possible, such that higher level classifications can be derived using
|
|
|
|
|
|
the Standardized Vocabularies.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="fact_relationship" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">fact_relationship</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The FACT_RELATIONSHIP table contains records about the relationships
|
|
|
|
|
|
between facts stored as records in any table of the CDM. Relationships
|
|
|
|
|
|
can be defined between facts from the same domain, or different domains.
|
|
|
|
|
|
Examples of Fact Relationships include: <a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms?domain=Relationship&standardConcept=Standard&page=2&pageSize=15&query=">Person
|
|
|
|
|
|
relationships</a> (parent-child), care site relationships (hierarchical
|
|
|
|
|
|
organizational structure of facilities within a health system),
|
|
|
|
|
|
indication relationship (between drug exposures and associated
|
|
|
|
|
|
conditions), usage relationships (of devices during the course of an
|
|
|
|
|
|
associated procedure), or facts derived from one another (measurements
|
|
|
|
|
|
derived from an associated specimen).</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>All relationships are directional, and each relationship is
|
|
|
|
|
|
represented twice symmetrically within the FACT_RELATIONSHIP table. For
|
|
|
|
|
|
example, two persons if person_id = 1 is the mother of person_id = 2 two
|
|
|
|
|
|
records are in the FACT_RELATIONSHIP table (all strings in fact
|
|
|
|
|
|
concept_id records in the Concept table: - Person, 1, Person, 2, parent
|
|
|
|
|
|
of - Person, 2, Person, 1, child of</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="survey_conduct" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">survey_conduct</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The SURVEY_CONDUCT table is used to store an instance of a completed
|
|
|
|
|
|
survey or questionnaire.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>This table captures details of the individual questionnaire such as
|
|
|
|
|
|
who completed it, when it was completed and to which patient treatment
|
|
|
|
|
|
or visit it relates to (if any).</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Each SURVEY has a SURVEY_CONCEPT_ID, a concept in the CONCEPT table
|
|
|
|
|
|
identifying the questionnaire e.g. EQ5D, VR12, SF12. Each questionnaire
|
|
|
|
|
|
should exist in the CONCEPT table. Each SURVEY can be optionally related
|
|
|
|
|
|
to a specific Visit in order to link it both to the Visit during which
|
|
|
|
|
|
it was completed and any subsequent Visit where treatment was assigned
|
|
|
|
|
|
based on the patient’s responses.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="location" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">location</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The LOCATION table represents a generic way to capture physical
|
|
|
|
|
|
location or address information of Persons and Care Sites. <strong>New
|
|
|
|
|
|
to CDM v6.0</strong> The LOCATION table now includes latitude and
|
|
|
|
|
|
longitude.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Each address or Location is unique and is present only once in the
|
|
|
|
|
|
table. Locations do not contain names, such as the name of a hospital.
|
|
|
|
|
|
In order to construct a full address that can be used in the postal
|
|
|
|
|
|
service, the address information from the Location needs to be combined
|
|
|
|
|
|
with information from the Care Site. For standardized geospatial
|
|
|
|
|
|
visualization and analysis, addresses need to be, at the minimum be
|
|
|
|
|
|
geocoded into latitude and longitude.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="location_history" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">location_history</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The LOCATION HISTORY table stores relationships between Persons or
|
|
|
|
|
|
Care Sites and geographic locations over time. <strong>This table is new
|
|
|
|
|
|
to CDM v6.0</strong></p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="care_site" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">care_site</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The CARE_SITE table contains a list of uniquely identified
|
|
|
|
|
|
institutional (physical or organizational) units where healthcare
|
|
|
|
|
|
delivery is practiced (offices, wards, hospitals, clinics, etc.).</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Care site is a unique combination of location_id and
|
|
|
|
|
|
place_of_service_source_value. Care site does not take into account the
|
|
|
|
|
|
provider (human) information such a specialty. Many source data do not
|
|
|
|
|
|
make a distinction between individual and institutional providers. The
|
|
|
|
|
|
CARE_SITE table contains the institutional providers. If the source,
|
|
|
|
|
|
instead of uniquely identifying individual Care Sites, only provides
|
|
|
|
|
|
limited information such as Place of Service, generic or “pooled” Care
|
|
|
|
|
|
Site records are listed in the CARE_SITE table. There can be
|
|
|
|
|
|
hierarchical and business relationships between Care Sites. For example,
|
|
|
|
|
|
wards can belong to clinics or departments, which can in turn belong to
|
|
|
|
|
|
hospitals, which in turn can belong to hospital systems, which in turn
|
|
|
|
|
|
can belong to HMOs.The relationships between Care Sites are defined in
|
|
|
|
|
|
the FACT_RELATIONSHIP table.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="provider" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">provider</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The PROVIDER table contains a list of uniquely identified healthcare
|
|
|
|
|
|
providers. These are individuals providing hands-on healthcare to
|
|
|
|
|
|
patients, such as physicians, nurses, midwives, physical therapists
|
|
|
|
|
|
etc.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Many sources do not make a distinction between individual and
|
|
|
|
|
|
institutional providers. The PROVIDER table contains the individual
|
|
|
|
|
|
providers. If the source, instead of uniquely identifying individual
|
|
|
|
|
|
providers, only provides limited information such as specialty, generic
|
|
|
|
|
|
or ‘pooled’ Provider records are listed in the PROVIDER table.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="payer_plan_period" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">payer_plan_period</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The PAYER_PLAN_PERIOD table captures details of the period of time
|
|
|
|
|
|
that a Person is continuously enrolled under a specific health Plan
|
|
|
|
|
|
benefit structure from a given Payer. Each Person receiving healthcare
|
|
|
|
|
|
is typically covered by a health benefit plan, which pays for (fully or
|
|
|
|
|
|
partially), or directly provides, the care. These benefit plans are
|
|
|
|
|
|
provided by payers, such as health insurances or state or government
|
|
|
|
|
|
agencies. In each plan the details of the health benefits are defined
|
|
|
|
|
|
for the Person or her family, and the health benefit Plan might change
|
|
|
|
|
|
over time typically with increasing utilization (reaching certain cost
|
|
|
|
|
|
thresholds such as deductibles), plan availability and purchasing
|
|
|
|
|
|
choices of the Person. The unique combinations of Payer organizations,
|
|
|
|
|
|
health benefit Plans and time periods in which they are valid for a
|
|
|
|
|
|
Person are recorded in this table.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>A Person can have multiple, overlapping, Payer_Plan_Periods in this
|
|
|
|
|
|
table. For example, medical and drug coverage in the US can be
|
|
|
|
|
|
represented by two Payer_Plan_Periods. The details of the benefit
|
|
|
|
|
|
structure of the Plan is rarely known, the idea is just to identify that
|
|
|
|
|
|
the Plans are different.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="cost" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">cost</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The COST table captures records containing the cost of any medical
|
|
|
|
|
|
event recorded in one of the OMOP clinical event tables such as
|
|
|
|
|
|
DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE, VISIT_DETAIL,
|
|
|
|
|
|
DEVICE_OCCURRENCE, OBSERVATION or MEASUREMENT.</p>
|
|
|
|
|
|
<p>Each record in the cost table account for the amount of money
|
|
|
|
|
|
transacted for the clinical event. So, the COST table may be used to
|
|
|
|
|
|
represent both receivables (charges) and payments (paid), each
|
|
|
|
|
|
transaction type represented by its COST_CONCEPT_ID. The
|
|
|
|
|
|
COST_TYPE_CONCEPT_ID field will use concepts in the Standardized
|
|
|
|
|
|
Vocabularies to designate the source (provenance) of the cost data. A
|
|
|
|
|
|
reference to the health plan information in the PAYER_PLAN_PERIOD table
|
|
|
|
|
|
is stored in the record for information used for the adjudication system
|
|
|
|
|
|
to determine the persons benefit for the clinical event.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>When dealing with summary costs, the cost of the goods or services
|
|
|
|
|
|
the provider provides is often not known directly, but derived from the
|
|
|
|
|
|
hospital charges multiplied by an average cost-to-charge ratio.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>One cost record is generated for each response by a payer. In a
|
|
|
|
|
|
claims databases, the payment and payment terms reported by the payer
|
|
|
|
|
|
for the goods or services billed will generate one cost record. If the
|
|
|
|
|
|
source data has payment information for more than one payer
|
|
|
|
|
|
(i.e. primary insurance and secondary insurance payment for one entity),
|
|
|
|
|
|
then a cost record is created for each reporting payer. Therefore, it is
|
|
|
|
|
|
possible for one procedure to have multiple cost records for each payer,
|
|
|
|
|
|
but typically it contains one or no record per entity. Payer
|
|
|
|
|
|
reimbursement cost records will be identified by using the PAYER_PLAN_ID
|
|
|
|
|
|
field. Drug costs are composed of ingredient cost (the amount charged by
|
|
|
|
|
|
the wholesale distributor or manufacturer), the dispensing fee (the
|
|
|
|
|
|
amount charged by the pharmacy and the sales tax).</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="drug_era" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">drug_era</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>A Drug Era is defined as a span of time when the Person is assumed to
|
|
|
|
|
|
be exposed to a particular active ingredient. A Drug Era is not the same
|
|
|
|
|
|
as a Drug Exposure: Exposures are individual records corresponding to
|
|
|
|
|
|
the source when Drug was delivered to the Person, while successive
|
|
|
|
|
|
periods of Drug Exposures are combined under certain rules to produce
|
|
|
|
|
|
continuous Drug Eras.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The SQL script for generating DRUG_ERA records can be found <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/sqlScripts.html#drug_eras">here</a>.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="dose_era" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">dose_era</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>A Dose Era is defined as a span of time when the Person is assumed to
|
|
|
|
|
|
be exposed to a constant dose of a specific active ingredient.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Dose Eras will be derived from records in the DRUG_EXPOSURE table and
|
|
|
|
|
|
the Dose information from the DRUG_STRENGTH table using a standardized
|
|
|
|
|
|
algorithm. Dose Form information is not taken into account. So, if the
|
|
|
|
|
|
patient changes between different formulations, or different
|
|
|
|
|
|
manufacturers with the same formulation, the Dose Era is still spanning
|
|
|
|
|
|
the entire time of exposure to the Ingredient.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="condition_era" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">condition_era</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>A Condition Era is defined as a span of time when the Person is
|
|
|
|
|
|
assumed to have a given condition. Similar to Drug Eras, Condition Eras
|
|
|
|
|
|
are chronological periods of Condition Occurrence. Combining individual
|
|
|
|
|
|
Condition Occurrences into a single Condition Era serves two
|
|
|
|
|
|
purposes:</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>It allows aggregation of chronic conditions that require frequent
|
|
|
|
|
|
ongoing care, instead of treating each Condition Occurrence as an
|
|
|
|
|
|
independent event.</li>
|
|
|
|
|
|
<li>It allows aggregation of multiple, closely timed doctor visits for
|
|
|
|
|
|
the same Condition to avoid double-counting the Condition Occurrences.
|
|
|
|
|
|
For example, consider a Person who visits her Primary Care Physician
|
|
|
|
|
|
(PCP) and who is referred to a specialist. At a later time, the Person
|
|
|
|
|
|
visits the specialist, who confirms the PCP’s original diagnosis and
|
|
|
|
|
|
provides the appropriate treatment to resolve the condition. These two
|
|
|
|
|
|
independent doctor visits should be aggregated into one Condition
|
|
|
|
|
|
Era.</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</ul>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Each Condition Era corresponds to one or many Condition Occurrence
|
|
|
|
|
|
records that form a continuous interval. The condition_concept_id field
|
|
|
|
|
|
contains Concepts that are identical to those of the
|
|
|
|
|
|
CONDITION_OCCURRENCE table records that make up the Condition Era. In
|
|
|
|
|
|
contrast to Drug Eras, Condition Eras are not aggregated to contain
|
|
|
|
|
|
Conditions of different hierarchical layers. The SQl Script for
|
|
|
|
|
|
generating CONDITION_ERA records can be found <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/sqlScripts.html#condition_eras">here</a>
|
|
|
|
|
|
The Condition Era Start Date is the start date of the first Condition
|
|
|
|
|
|
Occurrence. The Condition Era End Date is the end date of the last
|
|
|
|
|
|
Condition Occurrence. Condition Eras are built with a Persistence Window
|
|
|
|
|
|
of 30 days, meaning, if no occurrence of the same condition_concept_id
|
|
|
|
|
|
happens within 30 days of any one occurrence, it will be considered the
|
|
|
|
|
|
condition_era_end_date.</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="metadata" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">metadata</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The METADATA table contains metadata information about a dataset that
|
|
|
|
|
|
has been transformed to the OMOP Common Data Model.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="cdm_source" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">cdm_source</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The CDM_SOURCE table contains detail about the source database and
|
|
|
|
|
|
the process used to transform the data into the OMOP Common Data
|
|
|
|
|
|
Model.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="concept" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">concept</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The Standardized Vocabularies contains records, or Concepts, that
|
|
|
|
|
|
uniquely identify each fundamental unit of meaning used to express
|
|
|
|
|
|
clinical information in all domain tables of the CDM. Concepts are
|
|
|
|
|
|
derived from vocabularies, which represent clinical information across a
|
|
|
|
|
|
domain (e.g. conditions, drugs, procedures) through the use of codes and
|
|
|
|
|
|
associated descriptions. Some Concepts are designated Standard Concepts,
|
|
|
|
|
|
meaning these Concepts can be used as normative expressions of a
|
|
|
|
|
|
clinical entity within the OMOP Common Data Model and within
|
|
|
|
|
|
standardized analytics. Each Standard Concept belongs to one domain,
|
|
|
|
|
|
which defines the location where the Concept would be expected to occur
|
|
|
|
|
|
within data tables of the CDM.</p>
|
|
|
|
|
|
<p>Concepts can represent broad categories (like ‘Cardiovascular
|
|
|
|
|
|
disease’), detailed clinical elements (‘Myocardial infarction of the
|
|
|
|
|
|
anterolateral wall’) or modifying characteristics and attributes that
|
|
|
|
|
|
define Concepts at various levels of detail (severity of a disease,
|
|
|
|
|
|
associated morphology, etc.).</p>
|
|
|
|
|
|
<p>Records in the Standardized Vocabularies tables are derived from
|
|
|
|
|
|
national or international vocabularies such as SNOMED-CT, RxNorm, and
|
|
|
|
|
|
LOINC, or custom Concepts defined to cover various aspects of
|
|
|
|
|
|
observational data analysis.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="vocabulary" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">vocabulary</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The VOCABULARY table includes a list of the Vocabularies collected
|
|
|
|
|
|
from various sources or created de novo by the OMOP community. This
|
|
|
|
|
|
reference table is populated with a single record for each Vocabulary
|
|
|
|
|
|
source and includes a descriptive name and other associated attributes
|
|
|
|
|
|
for the Vocabulary.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="domain" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">domain</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The DOMAIN table includes a list of OMOP-defined Domains the Concepts
|
|
|
|
|
|
of the Standardized Vocabularies can belong to. A Domain defines the set
|
|
|
|
|
|
of allowable Concepts for the standardized fields in the CDM tables. For
|
|
|
|
|
|
example, the “Condition” Domain contains Concepts that describe a
|
|
|
|
|
|
condition of a patient, and these Concepts can only be stored in the
|
|
|
|
|
|
condition_concept_id field of the CONDITION_OCCURRENCE and CONDITION_ERA
|
|
|
|
|
|
tables. This reference table is populated with a single record for each
|
|
|
|
|
|
Domain and includes a descriptive name for the Domain.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="concept_class" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">concept_class</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The CONCEPT_CLASS table is a reference table, which includes a list
|
|
|
|
|
|
of the classifications used to differentiate Concepts within a given
|
|
|
|
|
|
Vocabulary. This reference table is populated with a single record for
|
|
|
|
|
|
each Concept Class.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<div id="concept_relationship"
|
|
|
|
|
|
class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">concept_relationship</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The CONCEPT_RELATIONSHIP table contains records that define direct
|
|
|
|
|
|
relationships between any two Concepts and the nature or type of the
|
|
|
|
|
|
relationship. Each type of a relationship is defined in the RELATIONSHIP
|
|
|
|
|
|
table.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="relationship" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">relationship</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The RELATIONSHIP table provides a reference list of all types of
|
|
|
|
|
|
relationships that can be used to associate any two concepts in the
|
|
|
|
|
|
CONCEPT_RELATIONSHP table.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
<div id="concept_synonym" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">concept_synonym</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The CONCEPT_SYNONYM table is used to store alternate names and
|
|
|
|
|
|
descriptions for Concepts.</p>
|
2023-10-26 18:13:30 +00:00
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<p><strong>User Guide</strong></p>
|
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<p>NA</p>
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<p><strong>ETL Conventions</strong></p>
|
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|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
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</div>
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<div id="concept_ancestor" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
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<h3 class="tabset tabset-pills">concept_ancestor</h3>
|
2020-10-06 15:11:13 +00:00
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|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
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<p>The CONCEPT_ANCESTOR table is designed to simplify observational
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analysis by providing the complete hierarchical relationships between
|
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|
Concepts. Only direct parent-child relationships between Concepts are
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stored in the CONCEPT_RELATIONSHIP table. To determine higher level
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ancestry connections, all individual direct relationships would have to
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be navigated at analysis time. The CONCEPT_ANCESTOR table includes
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records for all parent-child relationships, as well as
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grandparent-grandchild relationships and those of any other level of
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lineage. Using the CONCEPT_ANCESTOR table allows for querying for all
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descendants of a hierarchical concept. For example, drug ingredients and
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drug products are all descendants of a drug class ancestor.</p>
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<p>This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP
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and RELATIONSHIP tables.</p>
|
2023-10-26 18:13:30 +00:00
|
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|
<p><strong>User Guide</strong></p>
|
|
|
|
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|
<p>NA</p>
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|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
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|
|
</div>
|
2023-02-08 20:04:22 +00:00
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<div id="source_to_concept_map"
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class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
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|
<h3 class="tabset tabset-pills">source_to_concept_map</h3>
|
2020-10-06 15:11:13 +00:00
|
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|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The source to concept map table is a legacy data structure within the
|
|
|
|
|
|
OMOP Common Data Model, recommended for use in ETL processes to maintain
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local source codes which are not available as Concepts in the
|
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Standardized Vocabularies, and to establish mappings for each source
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code into a Standard Concept as target_concept_ids that can be used to
|
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populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table
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|
|
is no longer populated with content within the Standardized Vocabularies
|
|
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|
|
published to the OMOP community.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
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|
<div id="drug_strength" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">drug_strength</h3>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The DRUG_STRENGTH table contains structured content about the amount
|
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|
or concentration and associated units of a specific ingredient contained
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|
within a particular drug product. This table is supplemental information
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|
to support standardized analysis of drug utilization.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2021-01-06 15:52:57 +00:00
|
|
|
|
</div>
|
2021-09-23 14:52:05 +00:00
|
|
|
|
<div id="cohort" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
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|
<h3 class="tabset tabset-pills">cohort</h3>
|
2021-09-23 14:52:05 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The COHORT table contains records of subjects that satisfy a given
|
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|
|
set of criteria for a duration of time. The definition of the cohort is
|
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|
|
contained within the COHORT_DEFINITION table. It is listed as part of
|
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|
|
the RESULTS schema because it is a table that users of the database as
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|
well as tools such as ATLAS need to be able to write to. The CDM and
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|
Vocabulary tables are all read-only so it is suggested that the COHORT
|
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|
and COHORT_DEFINTION tables are kept in a separate schema to alleviate
|
|
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|
|
|
confusion.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2021-09-23 14:52:05 +00:00
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Cohorts typically include patients diagnosed with a specific
|
|
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|
condition, patients exposed to a particular drug, but can also be
|
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Providers who have performed a specific Procedure. Cohort records must
|
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|
have a Start Date and an End Date, but the End Date may be set to Start
|
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|
Date or could have an applied censor date using the Observation Period
|
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|
Start Date. Cohort records must contain a Subject Id, which can refer to
|
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|
|
the Person, Provider, Visit record or Care Site though they are most
|
|
|
|
|
|
often Person Ids. The Cohort Definition will define the type of subject
|
|
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|
|
through the subject concept id. A subject can belong (or not belong) to
|
|
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|
|
a cohort at any moment in time. A subject can only have one record in
|
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|
|
the cohort table for any moment of time, i.e. it is not possible for a
|
|
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|
|
person to contain multiple records indicating cohort membership that are
|
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|
|
overlapping in time</p>
|
2021-09-23 14:52:05 +00:00
|
|
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|
</div>
|
2021-01-06 15:52:57 +00:00
|
|
|
|
<div id="cohort_definition" class="section level3 tabset tabset-pills">
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<h3 class="tabset tabset-pills">cohort_definition</h3>
|
2021-01-06 15:52:57 +00:00
|
|
|
|
<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The COHORT_DEFINITION table contains records defining a Cohort
|
|
|
|
|
|
derived from the data through the associated description and syntax and
|
|
|
|
|
|
upon instantiation (execution of the algorithm) placed into the COHORT
|
|
|
|
|
|
table. Cohorts are a set of subjects that satisfy a given combination of
|
|
|
|
|
|
inclusion criteria for a duration of time. The COHORT_DEFINITION table
|
|
|
|
|
|
provides a standardized structure for maintaining the rules governing
|
|
|
|
|
|
the inclusion of a subject into a cohort, and can store operational
|
|
|
|
|
|
programming code to instantiate the cohort within the OMOP Common Data
|
|
|
|
|
|
Model.</p>
|
2023-10-26 18:13:30 +00:00
|
|
|
|
<p><strong>User Guide</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
|
|
|
|
|
<p><strong>ETL Conventions</strong></p>
|
|
|
|
|
|
<p>NA</p>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</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() {
|
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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2019-08-28 15:02:47 +00:00
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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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$(document).ready(function () {
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window.buildTabsets("TOC");
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$(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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<!-- code folding -->
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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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2021-01-06 15:52:57 +00:00
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2020-04-27 20:35:41 +00:00
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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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2019-08-28 15:02:47 +00:00
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