2022-07-25 19:27:08 +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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2023-02-08 20:04:22 +00:00
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<title> How to Request Changes to the CDM</title>
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2022-07-25 19:27:08 +00:00
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2023-03-28 16:28:17 +00:00
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<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
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2022-07-25 19:27:08 +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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<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-1.11.4/jquery-ui.min.js"></script>
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<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
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<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
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<script src="site_libs/navigation-1.1/tabsets.js"></script>
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<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
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<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
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<link href="site_libs/font-awesome-5.1.0/css/v4-shims.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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window.setTimeout(function() { hljs.initHighlighting(); }, 0);
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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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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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2022-07-25 19:27:08 +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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});
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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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2023-03-28 16:28:17 +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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2022-07-25 19:27:08 +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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2023-03-28 16:28:17 +00:00
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content: "\e258";
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2022-07-25 19:27:08 +00:00
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font-family: 'Glyphicons Halflings';
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2023-03-28 16:28:17 +00:00
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border: none;
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2022-07-25 19:27:08 +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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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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2023-02-08 20:04:22 +00:00
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<h1 class="title toc-ignore"><img src="ohdsi40x40.png"></img> How to
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Request Changes to the CDM</h1>
|
2022-07-25 19:27:08 +00:00
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</div>
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2023-02-08 20:04:22 +00:00
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<p>Are you in the right place? Please answer the questions in the <a
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href="cdmDecisionTree.html">decision tree</a> prior to beginning a CDM
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Request to make sure you aren’t missing something.</p>
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<p>As OHDSI is an open-source community working towards developing a
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Common Data Model that fulfills the needs of its users, it is often the
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case that changes need to be made to the model as the community and its
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research continues to mature. However, the number of people,
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institutions, and initiatives that rely on the OMOP CDM to advance the
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science of observational health has grown dramatically since its
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inception in 2015. Therefore, care must be taken when considering any
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update to the model, big or small. This document outlines the process
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that should be taken to ratify a change to the CDM.</p>
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<p><strong>If you would like guidance prior to starting this process,
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consider contacting us on our <a
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href="https://github.com/OHDSI/CommonDataModel">GitHub</a> or <a
|
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href="https://teams.microsoft.com/l/team/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/conversations?groupId=a6f2c516-e568-4974-8f1e-a7bdc2f997c5&tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5">Teams
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Channel</a>.</strong></p>
|
2022-07-25 19:27:08 +00:00
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<div id="scope" class="section level3">
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<h3>Scope</h3>
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<ul>
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<li>What kind of changes?
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<ul>
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<li>Minor, e.g. new field in existing table</li>
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<li>Major, e.g. breaking changes, additional tables</li>
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</ul></li>
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<li>Who can propose changes?
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<ul>
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<li>Individuals, OHDSI working groups, organizations</li>
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</ul></li>
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</ul>
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</div>
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<div id="step-1-proposal" class="section level2">
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<h2>Step 1: Proposal</h2>
|
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<p>Once a group or organization has decided on the update they would
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like made to the model, they must produce a document including the
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following:</p>
|
2022-07-25 19:27:08 +00:00
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<ol style="list-style-type: decimal">
|
2023-02-08 20:04:22 +00:00
|
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<li>A clear description of the change or addition including the User
|
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Guide and ETL Conventions in the same structure as what is present on
|
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the website for every table and field currently in the CDM.</li>
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<li>A clearly defined use case noting why the latest version of the OMOP
|
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CDM fails to adequately address said use case. This should include
|
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describing what you have already tried with the latest version of the
|
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OMOP CDM and why it does not meet your needs.</li>
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<li>An example of how the requested change or addition will be used in
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practice. This can be in the form of sample data, SQL code, a diagram,
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or text. The proposal can optionally include suggestions as to how other
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OHDSI tools (Achilles, DataQualityDashboard, Atlas, etc.) should work
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with your change or addition.</li>
|
2022-07-25 19:27:08 +00:00
|
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</ol>
|
2023-02-08 20:04:22 +00:00
|
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<p>Once the document is ready to submit, please email <a
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|
href="mailto:a58abde7.ohdsi.org@amer.teams.ms">CDM Proposals - Workgroup
|
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|
- Common Data Model</a>. This will go directly to a separate channel in
|
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the OHDSI Teams environment that is available to all members of the CDM
|
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Working Group. After submitting your document with your proposal to
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email listed above, someone in the OMOP CDM Working Group will respond
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to you within 2 weeks. The potential outcomes are as follows:</p>
|
2022-07-25 19:27:08 +00:00
|
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<ul>
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<li>Proposal merits further review (move on to next steps)</li>
|
2023-02-08 20:04:22 +00:00
|
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<li>Proposal is not ready for workgroup review due to one or more
|
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factors
|
2022-07-25 19:27:08 +00:00
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<ul>
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<li>Incomplete</li>
|
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<li>Insufficiently aligned with the OMOP framework</li>
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<li>Poorly described use case</li>
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</ul></li>
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</ul>
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</div>
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<div id="step-2-initial-presentation" class="section level2">
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<h2>Step 2: Initial Presentation</h2>
|
2023-02-08 20:04:22 +00:00
|
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<p>Should your proposals merit further review, the OMOP CDM Working
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Group will reach out to you to schedule a time for you to present your
|
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case at an upcoming meeting. You will be given 15-30 minutes to present
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your document and you can include anything you feel will help illustrate
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the need and your potential solution. The group will then discuss, ask
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questions, and potentially offer other solutions. Depending on the
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nature of the request, this may go over multiple sessions and you may be
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asked to make changes to your initial design. At the end of this process
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your proposal will then be put to consensus in the CDM WG. If the group
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decides no, they will give feedback describing why they did not feel
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your proposal should be accepted at this time. If the group decides yes,
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you move on to step 3.</p>
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2022-07-25 19:27:08 +00:00
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<p><strong>Potential Decision Criteria:</strong></p>
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<ul>
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2023-02-08 20:04:22 +00:00
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<li>If the change is foundational to OHDSI tools, then the proposal will
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be put to the larger community open to public comment</li>
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<li>How generalizable is your change? Can it be readily applied to other
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use cases?</li>
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<li>Are the proposed changes/additions well designed from a modeling
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perspective? Do they follow the existing OMOP CDM conventions?</li>
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<li>What are the consequences of the change? Are they potentially
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breaking changes or are they just changes to existing conventions? Will
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they require the remapping of existing OMOP datasources?</li>
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<li>How complicated is your change? Is it an addition of a field or
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multiple tables?</li>
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2022-07-25 19:27:08 +00:00
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</ul>
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</div>
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<div id="step-3-preliminary-decision" class="section level2">
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<h2>Step 3: Preliminary Decision</h2>
|
2023-02-08 20:04:22 +00:00
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<p>If the proposal is accepted in the preliminary decision, then a
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branch will be created in the CommonDataModel repository, based on the
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latest version of the OMOP CDM in use (currently v5.4). It will then be
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your responsibility to apply the change programmatically in this branch.
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This should include:</p>
|
2022-07-25 19:27:08 +00:00
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<ul>
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2023-02-08 20:04:22 +00:00
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<li>Updating the CSV file with the CDM specification, including the User
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Guide and ETL Conventions documentation</li>
|
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<li>Generating the DDL files with the change</li>
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<li>Testing the new DDL files in at least one supported environment</li>
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</ul>
|
2023-02-08 20:04:22 +00:00
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<p>Once the DDLs with the proposed change are created and tested, you
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should then ETL some data (either real or synthetic) into the new
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table/fields. Then, an example cohort should be created that utilizes
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the change or addition and clearly displays how it can be used in a real
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study. It is expected that during this stage the proposal will change as
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you work through your idea in a tangible environment.</p>
|
2022-07-25 19:27:08 +00:00
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<p><strong>Potential Decision Criteria:</strong></p>
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<ul>
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<li>How would you evaluate the quality of this new field/table?</li>
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<li>What characterizations would you perform?</li>
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<li>How would you perform a study using this new feature?</li>
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</ul>
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<p><strong>Potential Outcomes:</strong></p>
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<ul>
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<li>Proposal demonstrates merit for further consideration as:
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<ul>
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<li>a core data model change (move on to next steps)</li>
|
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<li>an extension (how do we deal with these/do we have ownership of
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them?)</li>
|
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</ul></li>
|
2023-02-08 20:04:22 +00:00
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<li>Proposal does not demonstrate merit for further consideration at
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this time, and:
|
2022-07-25 19:27:08 +00:00
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<ul>
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<li>recommend as a LOCAL extension</li>
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<li>recommend a different course</li>
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</ul></li>
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</ul>
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</div>
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|
<div id="step-4-final-presentation" class="section level2">
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<h2>Step 4: Final Presentation</h2>
|
2023-02-08 20:04:22 +00:00
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<p>After generating, testing, and implementing your proposal in a
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real-world environment the CDM working group will invite you again to
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present your findings in another 15-30 minute presentation. This should
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include learnings from the exercise and any updates made to the initial
|
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proposal.</p>
|
2022-07-25 19:27:08 +00:00
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</div>
|
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|
<div id="step-5-final-decision" class="section level2">
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|
<h2>Step 5: Final Decision</h2>
|
2023-02-08 20:04:22 +00:00
|
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<p>At this point, the working group liaisons will also take the proposal
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to other groups to elicit feedback. Then the CDM working group will vote
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and give a final decision on the proposed change. If ratified, the
|
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branch in the repository will be merged into the develop branch to be
|
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included in a next version of the OMOP Common Data Model.</p>
|
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<p>The change should initiate requests for features in tools. The end of
|
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|
this process should be a trigger for using the new feature as per the
|
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use case. The group should also produce at least one query for the query
|
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|
library on how to work with the new addition/change.</p>
|
2022-07-25 19:27:08 +00:00
|
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|
<div id="resources" class="section level3">
|
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|
|
<h3>Resources</h3>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>“Implementing & adopting a customized OMOP Common Data Model”
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|
|
|
(Melany Philofsky, OHDSI Symposium 2021) <a
|
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|
|
href="https://www.ohdsi.org/2021-global-symposium-showcase-18/"
|
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|
|
|
class="uri">https://www.ohdsi.org/2021-global-symposium-showcase-18/</a></p>
|
2022-07-25 19:27:08 +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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</div>
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<script>
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<script>
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