2024-04-22 21:03:25 +00:00
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<!DOCTYPE html>
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<html>
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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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<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
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<title> Types of OMOP CDM Additions</title>
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<script src="site_libs/header-attrs-2.25/header-attrs.js"></script>
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<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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<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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<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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<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
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<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
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<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
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<script src="site_libs/navigation-1.1/tabsets.js"></script>
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<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
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<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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<link 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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<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
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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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<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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<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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details > summary > p:only-child {
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display: inline;
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}
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pre code {
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padding: 0;
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}
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</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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border-left-color: #adb5bd;
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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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<script type="text/javascript">
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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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// 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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// 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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});
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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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.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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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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content: "\e258";
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font-family: 'Glyphicons Halflings';
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border: none;
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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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background-color: transparent;
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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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@media print {
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.toc-content {
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/* see https://github.com/w3c/csswg-drafts/issues/4434 */
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float: right;
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}
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}
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.toc-content {
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padding-left: 30px;
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padding-right: 40px;
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}
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div.main-container {
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max-width: 1200px;
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}
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div.tocify {
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width: 20%;
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max-width: 260px;
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max-height: 85%;
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}
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@media (min-width: 768px) and (max-width: 991px) {
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div.tocify {
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width: 25%;
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}
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}
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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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.tocify .list-group-item {
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border-radius: 0px;
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}
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</style>
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</head>
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<body>
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<div class="container-fluid main-container">
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<!-- setup 3col/9col grid for toc_float and main content -->
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<div class="row">
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<div class="col-xs-12 col-sm-4 col-md-3">
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<div id="TOC" class="tocify">
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</div>
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</div>
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<div class="toc-content col-xs-12 col-sm-8 col-md-9">
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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<div class="container">
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<div class="navbar-header">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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</button>
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<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
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</div>
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<div id="navbar" class="navbar-collapse collapse">
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<ul class="nav navbar-nav">
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<li>
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<a href="index.html">
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<span class="fa fa-house"></span>
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</a>
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="fa fa-landmark"></span>
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Background
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<h1 class="title toc-ignore"><img src="ohdsi40x40.png"></img> Types of
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OMOP CDM Additions</h1>
|
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</div>
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<p>While the OMOP CDM supports a diverse set of use cases and data
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types, we acknowledge that not all can be represented in the CDM in its
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current form. Based on your use case it may be necessary to modify just
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your database, create an expansion, or suggest changes to the model that
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will be incorporated into the next official version. This document
|
|
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describes the types of additions that can be made to the CDM and how
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they should be utilized by the community.</p>
|
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<div id="site---specific-add-on" class="section level2">
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<h2>Site - Specific Add on</h2>
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<p>It is entirely within your rights as a data owner or holder to create
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additional columns or even tables in your own instance of your CDM that
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is specific to your site. However, they are not supported or recognized
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by OHDSI tools and not part of the canonical OMOP CDM. The Add on column
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or table is used for a site specific use case or data element. Examples
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include: privacy flags, source table identifiers or other data elements.
|
|
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|
|
See <a
|
|
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|
|
href="https://www.ohdsi.org/wp-content/uploads/2021/09/18-Implementing-Adopting-a-Customized-OMOP-Common-Data-Model.pdf">this
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poster</a> for background information and an implementation guide.</p>
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</div>
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<div id="expansionextension" class="section level2">
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<h2>Expansion/Extension</h2>
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<p>These are typically sets of tables created by working groups to model
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a specific type of data. The idea is that these tables follow the
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general conventions of the OMOP CDM but are not part of the canonical
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data model and therefore do not fall under the purview of the CDM
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|
working group. They are developed using OMOP conventions applied to
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domain specific datasets. It is possible they could become part of the
|
|
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|
CDM in the future (like the episode and episode_event tables) but that
|
|
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|
is not a given. If using an expansion/extension with your data they are
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invisible to the tools. They can be used as part of network research but
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you would need to ensure that all participating databases are using the
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extension/expansion before writing a study package that incorporates the
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tables.</p>
|
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|
<p><strong>Examples include:</strong></p>
|
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<ul>
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|
<li>Oncology
|
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<ul>
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<li>Github: <a href="https://ohdsi.github.io/OncologyWG/"
|
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class="uri">https://ohdsi.github.io/OncologyWG/</a></li>
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</ul></li>
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<li>Medical Imaging
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<ul>
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<li>Github: <a href="https://github.com/paulnagy/DICOM2OMOP"
|
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|
class="uri">https://github.com/paulnagy/DICOM2OMOP</a></li>
|
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<li>Paper: <a
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|
href="https://link-springer-com.ezjandj.infotrieve.com/article/10.1007/s10278-024-00982-6"
|
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class="uri">https://link-springer-com.ezjandj.infotrieve.com/article/10.1007/s10278-024-00982-6</a></li>
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</ul></li>
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<li>GIS
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<ul>
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<li>Github: <a href="https://ohdsi.github.io/GIS/"
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class="uri">https://ohdsi.github.io/GIS/</a></li>
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</ul></li>
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</ul>
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</div>
|
2024-04-23 14:32:31 +00:00
|
|
|
<div id="change-to-canonical-cdm" class="section level2">
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<h2>Change to Canonical CDM</h2>
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|
<p>Please see the <a href="/CommonDataModel/cdmRequestProcess.html">full
|
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|
|
process</a> for how to request changes to the current version of the
|
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|
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|
OMOP CDM. These change requests MUST be backed by network uses cases and
|
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|
MUST be approved by the <a
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|
href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu">CDM
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|
working group</a>. Overall these are typically small changes or
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additions that make the CDM more usable from a network perspective or
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|
fulfill a clearly demonstrated need. Good examples are the recently
|
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|
ratified <a
|
2024-04-22 21:03:25 +00:00
|
|
|
href="https://github.com/OHDSI/CommonDataModel/tree/NLP_Proposal_2023">NOTE_NLP
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updates</a> and presentation by the vocabulary team to add <a
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|
href="https://ohdsiorg.sharepoint.com/:v:/s/Workgroup-CommonDataModel/EcMaYjUPeSVMrmSozflBsmQBNEtPpiCJ9AfZ3QQtGHIuFg?e=UnVgIh&nav=eyJyZWZlcnJhbEluZm8iOnsicmVmZXJyYWxBcHAiOiJTdHJlYW1XZWJBcHAiLCJyZWZlcnJhbFZpZXciOiJTaGFyZURpYWxvZy1MaW5rIiwicmVmZXJyYWxBcHBQbGF0Zm9ybSI6IldlYiIsInJlZmVycmFsTW9kZSI6InZpZXcifX0%3D">value_source_concept_id</a>
|
2024-04-23 14:32:31 +00:00
|
|
|
to the measurement and observation tables.</p>
|
2024-04-22 21:03:25 +00:00
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</div>
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</div>
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</div>
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</div>
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<script>
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// add bootstrap table styles to pandoc tables
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function bootstrapStylePandocTables() {
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$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
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}
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$(document).ready(function () {
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bootstrapStylePandocTables();
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</script>
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<script>
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$(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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});
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</script>
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<!-- code folding -->
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<script>
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$(document).ready(function () {
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// temporarily add toc-ignore selector to headers for the consistency with Pandoc
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$('.unlisted.unnumbered').addClass('toc-ignore')
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// move toc-ignore selectors from section div to header
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$('div.section.toc-ignore')
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.removeClass('toc-ignore')
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.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
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// establish options
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// tocify
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var toc = $("#TOC").tocify(options).data("toc-tocify");
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