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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2022-01-13 18:59:03 +00:00
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<title>dataModelConventions.knit</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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2022-07-27 01:48:28 +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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2022-07-27 01:48:28 +00:00
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details > summary > p:only-child {
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display: inline;
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}
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2022-01-13 18:59:03 +00:00
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pre code {
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padding: 0;
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}
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2019-08-28 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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2020-10-06 15:11:13 +00:00
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<div id="data-model-conventions" class="section level1">
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<h1><strong>Data Model Conventions</strong></h1>
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2023-02-08 20:04:22 +00:00
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<p>There are a number of implicit and explicit conventions that have
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been adopted in the CDM. Developers of methods that run against the CDM
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need to understand these conventions.</p>
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2020-10-06 15:11:13 +00:00
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<div id="general" class="section level2">
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<h2><strong>General</strong></h2>
|
2023-02-08 20:04:22 +00:00
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<p>The OMOP CDM is platform-independent. Data types are defined
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generically using ANSI SQL data types (VARCHAR, INTEGER, FLOAT, DATE,
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DATETIME, CLOB). Precision is provided only for VARCHAR. It reflects the
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minimal required string length and can be expanded within a CDM
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instantiation. The CDM does not prescribe the date and datetime format.
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Standard queries against CDM may vary for local instantiations and
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date/datetime configurations.</p>
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2020-10-06 15:11:13 +00:00
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<div id="tables" class="section level3">
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<h3>Tables</h3>
|
2023-02-08 20:04:22 +00:00
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<p>For the tables of the main domains of the CDM it is imperative that
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concepts used are strictly limited to the domain. For example, the
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CONDITION_OCCURRENCE table contains only information about conditions
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(diagnoses, signs, symptoms), but no information about procedures. Not
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all source coding schemes adhere to such rules. For example, ICD-9-CM
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codes, which contain mostly diagnoses of human disease, also contain
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information about the status of patients having received a procedure.
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The ICD-9-CM code V20.3 ‘Newborn health supervision’ defines a
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continuous procedure and is therefore stored in the PROCEDURE_OCCURRENCE
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table.</p>
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</div>
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2020-10-06 15:11:13 +00:00
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<div id="fields" class="section level3">
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<h3>Fields</h3>
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2019-08-28 15:02:47 +00:00
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<p>Variable names across all tables follow one convention:</p>
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<table>
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<colgroup>
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<col width="29%" />
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<col width="70%" />
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</colgroup>
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<thead>
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<tr class="header">
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<th>Notation</th>
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<th>Description</th>
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</tr>
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</thead>
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<tbody>
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<tr class="odd">
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<td><entity>_SOURCE_VALUE</td>
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<td>Verbatim information from the source data, typically used in ETL to
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map to CONCEPT_ID, and not to be used by any standard analytics. For
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example, CONDITION_SOURCE_VALUE = ‘787.02’ was the ICD-9 code captured
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as a diagnosis from the administrative claim.</td>
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2019-08-28 15:02:47 +00:00
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</tr>
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<tr class="even">
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<td><entity>_ID</td>
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<td>Unique identifiers for key entities, which can serve as foreign keys
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to establish relationships across entities. For example, PERSON_ID
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uniquely identifies each individual. VISIT_OCCURRENCE_ID uniquely
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identifies a PERSON encounter at a point of care.</td>
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2019-08-28 15:02:47 +00:00
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</tr>
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<tr class="odd">
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<td><entity>_CONCEPT_ID</td>
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<td>Foreign key into the Standardized Vocabularies (i.e. the
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standard_concept attribute for the corresponding term is true), which
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serves as the primary basis for all standardized analytics. For example,
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CONDITION_CONCEPT_ID = <a
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href="http://athena.ohdsi.org/search-terms/terms/31967">31967</a>
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contains the reference value for the SNOMED concept of ‘Nausea’</td>
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2019-08-28 15:02:47 +00:00
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</tr>
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<tr class="even">
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<td><entity>_SOURCE_CONCEPT_ID</td>
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<td>Foreign key into the Standardized Vocabularies representing the
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concept and terminology used in the source data, when applicable. For
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example, CONDITION_SOURCE_CONCEPT_ID = <a
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href="http://athena.ohdsi.org/search-terms/terms/45431665">45431665</a>
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denotes the concept of ‘Nausea’ in the Read terminology; the analogous
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CONDITION_CONCEPT_ID might be 31967, since SNOMED-CT is the Standardized
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Vocabulary for most clinical diagnoses and findings.</td>
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2019-08-28 15:02:47 +00:00
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</tr>
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<tr class="odd">
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<td><entity>_TYPE_CONCEPT_ID</td>
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<td>Delineates the origin of the source information, standardized within
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the Standardized Vocabularies. For example, DRUG_TYPE_CONCEPT_ID can
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allow analysts to discriminate between ‘Pharmacy dispensing’ and
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‘Prescription written’</td>
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2019-08-28 15:02:47 +00:00
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</tr>
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</tbody>
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</table>
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</div>
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2020-10-06 15:11:13 +00:00
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</div>
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<div id="vocabulary" class="section level2">
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<h2><strong>Vocabulary</strong></h2>
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<div id="concepts" class="section level3">
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<h3>Concepts</h3>
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2023-02-08 20:04:22 +00:00
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<p>Concepts in the Common Data Model are derived from a number of public
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or proprietary terminologies such as SNOMED-CT and RxNorm, or custom
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generated to standardize aspects of observational data. Both types of
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Concepts are integrated based on the following rules:</p>
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2020-10-06 15:11:13 +00:00
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<ul>
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2023-02-08 20:04:22 +00:00
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<li>All Concepts are maintained centrally by the CDM and Vocabularies
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Working Group. Additional concepts can be added, as needed, upon request
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by creating a <a
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href="https://github.com/OHDSI/Vocabulary-v5.0/issues">Github
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issue</a>.</li>
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<li>For all Concepts, whether they are custom generated or adopted from
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published terminologies, a unique numeric identifier concept_id is
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assigned and used as the key to link all observational data to the
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corresponding Concept reference data.</li>
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<li>The concept_id of a Concept is persistent, i.e. stays the same for
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the same Concept between releases of the Standardized Vocabularies.</li>
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<li>A descriptive name for each Concept is stored as the Concept Name as
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part of the CONCEPT table. Additional names and descriptions for the
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Concept are stored as Synonyms in the <a
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href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym">CONCEPT_SYNONYM</a>
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table.</li>
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<li>Each Concept is assigned to a Domain. For Standard Concepts, there
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is always a single Domain. Source Concepts can be composite or
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coordinated entities, and therefore can belong to more than one Domain.
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The domain_id field of the record contains the abbreviation of the
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Domain, or Domain combination. Please refer to the Standardized
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Vocabularies specification for details of the Domain Assignment.</li>
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<li>Concept Class designations are attributes of Concepts. Each
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Vocabulary has its own set of permissible Concept Classes, although the
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same Concept Class can be used by more than one Vocabulary. Depending on
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the Vocabulary, the Concept Class may categorize Concepts vertically
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(parallel) or horizontally (hierarchically). See the specification of
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each vocabulary for details.</li>
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<li>Concept Class attributes should not be confused with Classification
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Concepts. These are separate Concepts that have a hierarchical
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relationship to Standard Concepts or each other, while Concept Classes
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are unique Vocabulary-specific attributes for each Concept.</li>
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<li>For Concepts inherited from published terminologies, the source code
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is retained in the concept_code field and can be used to reference the
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source vocabulary.</li>
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<li>Standard Concepts (designated as ‘S’ in the standard_concept field)
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may appear in CDM tables in all *_concept_id fields, whereas
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Classification Concepts (‘C’) should not appear in the CDM data, but
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participate in the construction of the CONCEPT_ANCESTOR table and can be
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used to identify Descendants that may appear in the data. See
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CONCEPT_ANCESTOR table. Non-standard Concepts can only appear in
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*_source_concept_id fields and are not used in <a
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href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a>
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table. Please refer to the Standardized Vocabularies specifications for
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details of the Standard Concept designation.</li>
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<li>The lifespan of a Concept is recorded through its valid_start_date,
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valid_end_date and the invalid_ reason fields. This allows Concepts to
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correctly reflect at which point in time were defined. Usually, Concepts
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get deprecated if their meaning was deemed ambiguous, a duplication of
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another Concept, or needed revision for scientific reason. For example,
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drug ingredients get updated when different salt or isomer variants
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enter the market. Usually, drugs taken off the market do not cause a
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deprecation by the terminology vendor. Since observational data are
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valid with respect to the time they are recorded, it is key for the
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Standardized Vocabularies to provide even obsolete codes and maintain
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their relationships to other current Concepts .</li>
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<li>Concepts without a known instantiated date are assigned
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valid_start_date of ‘1-Jan-1970’.</li>
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<li>Concepts that are not invalid are assigned valid_end_date of
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‘31-Dec-2099’.</li>
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<li>Deprecated Concepts (with a valid_end_date before the release date
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of the Standardized Vocabularies) will have a value of ‘D’ (deprecated
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without successor) or ‘U’ (updated). The updated Concepts have a record
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in the CONCEPT_RELATIONSHIP table indicating their active replacement
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Concept.</li>
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<li>Values for concept_ids generated as part of Standardized
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Vocabularies will be reserved from 0 to 2,000,000,000. Above this range,
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concept_ids are available for local use and are guaranteed not to clash
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with future releases of the Standardized Vocabularies.</li>
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2020-10-06 15:11:13 +00:00
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</ul>
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</div>
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<div id="vocabularies" class="section level3">
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<h3>Vocabularies</h3>
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<ul>
|
2023-02-08 20:04:22 +00:00
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<li>There is one record for each Vocabulary. One Vocabulary source or
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vendor can issue several Vocabularies, each of them creating their own
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record in the VOCABULARY table. However, the choice of whether a
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Vocabulary contains Concepts of different Concept Classes, or when these
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different classes constitute separate Vocabularies cannot precisely be
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decided based on the definition of what constitutes a Vocabulary. For
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example, the ICD-9 Volume 1 and 2 codes (ICD9CM, containing
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predominantly conditions and some procedures and observations) and the
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ICD-9 Volume 3 codes (ICD9Proc, containing predominantly procedures) are
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realized as two different Vocabularies. On the other hand, SNOMED-CT
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codes of the class Condition and those of the class Procedure are part
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of one and the same Vocabulary. Please refer to the Standardized
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Vocabularies specifications for details of each Vocabulary.</li>
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<li>The vocabulary_id field contains an alphanumerical identifier, that
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can also be used as the abbreviation of the Vocabulary name.</li>
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<li>The record with vocabulary_id = ‘None’ is reserved to contain
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information regarding the current version of the Entire Standardized
|
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Vocabularies.</li>
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<li>The vocabulary_name field contains the full official name of the
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Vocabulary, as well as the source or vendor in parenthesis.</li>
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<li>Each Vocabulary has an entry in the CONCEPT table, which is recorded
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in the vocabulary_concept_id field. This is for purposes of creating a
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closed Information Model, where all entities in the OMOP CDM are covered
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by a unique Concept.</li>
|
2020-10-06 15:11:13 +00:00
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</ul>
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</div>
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<div id="domains" class="section level3">
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<h3>Domains</h3>
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<ul>
|
2023-02-08 20:04:22 +00:00
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<li>There is one record for each Domain. The domains are defined by the
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tables and fields in the OMOP CDM that can contain Concepts describing
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all the various aspects of the healthcare experience of a patient.</li>
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<li>The domain_id field contains an alphanumerical identifier, that can
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also be used as the abbreviation of the Domain.</li>
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<li>The domain_name field contains the unabbreviated names of the
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Domain.</li>
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<li>Each Domain also has an entry in the Concept table, which is
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recorded in the domain_concept_id field. This is for purposes of
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creating a closed Information Model, where all entities in the OMOP CDM
|
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are covered by unique Concept.</li>
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<li>Versions prior to v5.0.0 of the OMOP CDM did not support the notion
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of a Domain.</li>
|
2020-10-06 15:11:13 +00:00
|
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</ul>
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</div>
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|
<div id="concept-classes" class="section level3">
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<h3>Concept Classes</h3>
|
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<ul>
|
2023-02-08 20:04:22 +00:00
|
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<li>There is one record for each Concept Class. Concept Classes are used
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to create additional structure to the Concepts within each Vocabulary.
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Some Concept Classes are unique to a Vocabulary (for example “Clinical
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Finding” in SNOMED), but others can be used across different
|
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|
|
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Vocabularies. The separation of Concepts through Concept Classes can be
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semantically horizontal (each Class subsumes Concepts of the same
|
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hierarchical level, akin to sub-Vocabularies within a Vocabulary) or
|
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vertical (each Class subsumes Concepts of a certain kind, going across
|
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|
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hierarchical levels). For example, Concept Classes in SNOMED are
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vertical: The classes “Procedure” and “Clinical Finding” define very
|
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granular to very generic Concepts. On the other hand, “Clinical Drug”
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and “Ingredient” Concept Classes define horizontal layers or strata in
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the RxNorm vocabulary, which all belong to the same concept of a
|
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Drug.</li>
|
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|
<li>The concept_class_id field contains an alphanumerical identifier,
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|
|
that can also be used as the abbreviation of the Concept Class.</li>
|
|
|
|
|
|
<li>The concept_class_name field contains the unabbreviated names of the
|
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|
|
Concept Class.</li>
|
|
|
|
|
|
<li>Each Concept Class also has an entry in the Concept table, which is
|
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|
|
|
|
recorded in the concept_ class_concept_id field. This is for purposes of
|
|
|
|
|
|
creating a closed Information Model, where all entities in the OMOP CDM
|
|
|
|
|
|
are covered by unique Concepts.</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</ul>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
<div id="concept-relationships" class="section level3">
|
|
|
|
|
|
<h3>Concept Relationships</h3>
|
|
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Relationships can generally be classified as hierarchical
|
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|
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(parent-child) or non-hierarchical (lateral).</li>
|
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|
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|
|
<li>All Relationships are directional, and each Concept Relationship is
|
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|
represented twice symmetrically within the CONCEPT_RELATIONSHIP table.
|
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|
For example, the two SNOMED concepts of ‘Acute myocardial infarction of
|
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|
|
the anterior wall’ and ‘Acute myocardial infarction’ have two Concept
|
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|
|
|
|
Relationships:
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>‘Acute myocardial infarction of the anterior wall’ ‘Is a’ ‘Acute
|
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|
|
myocardial infarction’, and</li>
|
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|
|
<li>‘Acute myocardial infarction’ ‘Subsumes’ ‘Acute myocardial
|
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|
|
infarction of the anterior wall’.</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</ul></li>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>There is one record for each Concept Relationship connecting the
|
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|
|
|
|
same Concepts with the same relationship_id.</li>
|
|
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|
|
<li>Since all Concept Relationships exist with their mirror image
|
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|
|
(concept_id_1 and concept_id_2 swapped, and the relationship_id replaced
|
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|
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|
|
by the reverse_relationship_id from the RELATIONSHIP table), it is not
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|
|
|
|
necessary to query for the existence of a relationship both in the
|
|
|
|
|
|
concept_id_1 and concept_id_2 fields.</li>
|
|
|
|
|
|
<li>Concept Relationships define direct relationships between Concepts.
|
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|
|
|
Indirect relationships through 3rd Concepts are not captured in this
|
|
|
|
|
|
table. However, the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a>
|
2024-03-28 19:09:22 +00:00
|
|
|
|
table does this for hierarchical relationships over several
|
|
|
|
|
|
“generations” of direct relationships.</li>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>In previous versions of the CDM, the relationship_id used to be a
|
|
|
|
|
|
numerical identifier. See the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#relationship">RELATIONSHIP</a>
|
|
|
|
|
|
table.</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</ul>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
<div id="relationship-table" class="section level3">
|
|
|
|
|
|
<h3>Relationship Table</h3>
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>There is one record for each Relationship.</li>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Relationships are classified as hierarchical (parent-child) or
|
|
|
|
|
|
non-hierarchical (lateral)</li>
|
|
|
|
|
|
<li>They are used to determine which concept relationship records should
|
|
|
|
|
|
be included in the computation of the CONCEPT_ANCESTOR table.</li>
|
|
|
|
|
|
<li>The relationship_id field contains an alphanumerical identifier,
|
|
|
|
|
|
that can also be used as the abbreviation of the Relationship.</li>
|
|
|
|
|
|
<li>The relationship_name field contains the unabbreviated names of the
|
|
|
|
|
|
Relationship.</li>
|
|
|
|
|
|
<li>Relationships all exist symmetrically, i.e. in both direction. The
|
|
|
|
|
|
relationship_id of the opposite Relationship is provided in the
|
|
|
|
|
|
reverse_relationship_id field.</li>
|
|
|
|
|
|
<li>Each Relationship also has an equivalent entry in the Concept table,
|
|
|
|
|
|
which is recorded in the relationship_ concept_id field. This is for
|
|
|
|
|
|
purposes of creating a closed Information Model, where all entities in
|
|
|
|
|
|
the OMOP CDM are covered by unique Concepts.</li>
|
|
|
|
|
|
<li>Hierarchical Relationships are used to build a hierarchical tree out
|
|
|
|
|
|
of the Concepts, which is recorded in the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a>
|
|
|
|
|
|
table. For example, “has_ingredient” is a Relationship between Concept
|
|
|
|
|
|
of the Concept Class ‘Clinical Drug’ and those of ‘Ingredient’, and all
|
|
|
|
|
|
Ingredients can be classified as the “parental” hierarchical Concepts
|
|
|
|
|
|
for the drug products they are part of. All ‘Is a’ Relationships are
|
|
|
|
|
|
hierarchical.</li>
|
|
|
|
|
|
<li>Relationships, also hierarchical, can be between Concepts within the
|
|
|
|
|
|
same Vocabulary or those adopted from different Vocabulary sources.</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</ul>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
<div id="concept-synonyms" class="section level3">
|
|
|
|
|
|
<h3>Concept Synonyms</h3>
|
|
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>The concept_synonym_name field contains a valid Synonym of a
|
|
|
|
|
|
concept, including the description in the concept_name itself. I.e. each
|
|
|
|
|
|
Concept has at least one Synonym in the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym">CONCEPT_SYNONYM</a>
|
|
|
|
|
|
table. As an example, for a SNOMED-CT Concept, if the fully specified
|
|
|
|
|
|
name is stored as the concept_name of the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept">CONCEPT</a>
|
|
|
|
|
|
table, then the Preferred Term and Synonyms associated with the Concept
|
|
|
|
|
|
are stored in the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym">CONCEPT_SYNONYM</a>
|
|
|
|
|
|
table.</li>
|
|
|
|
|
|
<li>Only Synonyms that are active and current are stored in the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_synonym">CONCEPT_SYNONYM</a>
|
|
|
|
|
|
table. Tracking synonym/description history and mapping of obsolete
|
|
|
|
|
|
synonyms to current Concepts/Synonyms is out of scope for the Standard
|
|
|
|
|
|
Vocabularies.</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<li>Currently, only English Synonyms are included.</li>
|
|
|
|
|
|
</ul>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
<div id="concept-ancestor" class="section level3">
|
|
|
|
|
|
<h3>Concept Ancestor</h3>
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>Each concept is also recorded as an ancestor of itself.</li>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Only valid and Standard Concepts participate in the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a>
|
|
|
|
|
|
table. It is not possible to find ancestors or descendants of deprecated
|
|
|
|
|
|
or Source Concepts.</li>
|
|
|
|
|
|
<li>Usually, only Concepts of the same Domain are connected through
|
|
|
|
|
|
records of the <a
|
|
|
|
|
|
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a>
|
|
|
|
|
|
table, but there might be exceptions.</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</ul>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
<div id="source-to-concept-map" class="section level3">
|
|
|
|
|
|
<h3>Source to Concept Map</h3>
|
|
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>This table is no longer used to distribute mapping information
|
|
|
|
|
|
between source codes and Standard Concepts for the Standard
|
|
|
|
|
|
Vocabularies. Instead, the CONCEPT_RELATIONSHIP table is used for this
|
|
|
|
|
|
purpose, using the relationship_id=‘Maps to’.</li>
|
|
|
|
|
|
<li>However, this table can still be used for the translation of local
|
|
|
|
|
|
source codes into Standard Concepts.</li>
|
|
|
|
|
|
<li><strong>Note:</strong> This table should not be used to translate
|
|
|
|
|
|
source codes to Source Concepts. The source code of a Source Concept is
|
|
|
|
|
|
captured in its concept_code field. If the source codes used in a given
|
|
|
|
|
|
database do not follow correct formatting the ETL will have to perform
|
|
|
|
|
|
this translation. For example, if ICD-9-CM codes are recorded without a
|
|
|
|
|
|
dot the ETL will have to perform a lookup function that allows
|
|
|
|
|
|
identifying the correct ICD-9-CM Source Concept (with the dot in the
|
|
|
|
|
|
concept_code field).</li>
|
|
|
|
|
|
<li>The source_concept_id, or the combination of the fields source_code
|
|
|
|
|
|
and the source_vocabulary_id uniquely identifies the source information.
|
|
|
|
|
|
It is the equivalent to the concept_id_1 field in the
|
|
|
|
|
|
CONCEPT_RELATIONSHIP table.</li>
|
|
|
|
|
|
<li>If there is no source_concept_id available because the source codes
|
|
|
|
|
|
are local and not supported by the Standard Vocabulary, the content of
|
|
|
|
|
|
the field is 0 (zero, not null) encoding an undefined concept. However,
|
|
|
|
|
|
local Source Concepts are established (concept_id values above
|
|
|
|
|
|
2,000,000,000).</li>
|
|
|
|
|
|
<li>The source_code_description contains an optional description of the
|
|
|
|
|
|
source code.</li>
|
|
|
|
|
|
<li>The target_concept_id contains the Concept the source code is mapped
|
|
|
|
|
|
to. It is equivalent to the concept_id_2 in the CONCEPT_RELATIONSHIP
|
|
|
|
|
|
table</li>
|
|
|
|
|
|
<li>The target_vocabulary_id field contains the vocabulary_id of the
|
|
|
|
|
|
target concept. It is a duplication of the same information in the
|
|
|
|
|
|
CONCEPT record of the Target Concept.</li>
|
|
|
|
|
|
<li>The fields valid_start_date, valid_end_date and invalid_reason are
|
|
|
|
|
|
used to define the life cycle of the mapping information. Invalid
|
|
|
|
|
|
mapping records should not be used for mapping information.</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</ul>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
<div id="drug-strength" class="section level3">
|
|
|
|
|
|
<h3>Drug Strength</h3>
|
|
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>The DRUG_STRENGTH table contains information for each active
|
|
|
|
|
|
(non-deprecated) Standard Drug Concept.</li>
|
|
|
|
|
|
<li>A drug which contains multiple active Ingredients will result in
|
|
|
|
|
|
multiple DRUG_STRENGTH records, one for each active ingredient.</li>
|
|
|
|
|
|
<li>Ingredient strength information is provided either as absolute
|
|
|
|
|
|
amount (usually for solid formulations) or as concentration (usually for
|
|
|
|
|
|
liquid formulations).</li>
|
|
|
|
|
|
<li>If the absolute amount is provided (for example, ‘Acetaminophen 5 MG
|
|
|
|
|
|
Tablet’) the amount_value and amount_unit_concept_id are used to define
|
|
|
|
|
|
this content (in this case 5 and ‘MG’).</li>
|
|
|
|
|
|
<li>If the concentration is provided (for example ‘Acetaminophen 48
|
|
|
|
|
|
MG/ML Oral Solution’) the numerator_ value in combination with the
|
|
|
|
|
|
numerator_unit_concept_id and denominator_unit_concept_id are used to
|
|
|
|
|
|
define this content (in this case 48, ‘MG’ and ‘ML’).</li>
|
|
|
|
|
|
<li>In case of Quantified Clinical or Branded Drugs the
|
|
|
|
|
|
denominator_value contains the total amount of the solution (not the
|
|
|
|
|
|
amount of the ingredient). In all other drug concept classes the
|
|
|
|
|
|
denominator amount is NULL because the concentration is always
|
|
|
|
|
|
normalized to the unit of the denominator. So, a product containing 960
|
|
|
|
|
|
mg in 20 mL is provided as 48 mg/mL in the Clinical Drug and Clinical
|
|
|
|
|
|
Drug Component, while as a Quantified Clinical Drug it is written as 960
|
|
|
|
|
|
mg/20 mL.</li>
|
|
|
|
|
|
<li>If the strength is provided in % (volume or mass-percent are not
|
|
|
|
|
|
distinguished) it is stored in the
|
|
|
|
|
|
numerator_value/numerator_unit_concept_id field combination, with both
|
|
|
|
|
|
the denominator_value and denominator_unit_concept_id set to NULL. If it
|
|
|
|
|
|
is a Quantified Drug the total amount of drug is provided in the
|
|
|
|
|
|
denominator_value/denominator_unit_concept_id pair. E.g., the 30 G
|
|
|
|
|
|
Isoconazole 2% Topical Cream is provided as 2% / in Clinical Drug and
|
|
|
|
|
|
Clinical Drug Component, and as 2% /30 G.</li>
|
|
|
|
|
|
<li>Sometimes, one Ingredient is listed with different units within the
|
|
|
|
|
|
same drug. This is very rare, and usually this happens if there are more
|
|
|
|
|
|
than one Precise Ingredient. For example, ‘Penicillin G, 30 Benzathine
|
|
|
|
|
|
150000 UNT/ML / Penicillin G, Procaine 150000 MEQ/ML Injectable
|
|
|
|
|
|
Suspension’ contains Penicillin G in two different forms.</li>
|
|
|
|
|
|
<li>Sometimes, different ingredients in liquid drugs are listed with
|
|
|
|
|
|
different units in the denominator_ unit_concept_id. This is usually the
|
|
|
|
|
|
case if the ingredients are liquids themselves (concentration provided
|
|
|
|
|
|
as mL/mL) or solid substances (mg/mg). In these cases, the general
|
|
|
|
|
|
assumptions is made that the density of the drug is that of water, and
|
|
|
|
|
|
one can assume 1 g = 1 mL.</li>
|
|
|
|
|
|
<li>All Drug vocabularies containing Standard Concepts have entries in
|
|
|
|
|
|
the DRUG_STRENGTH table.</li>
|
|
|
|
|
|
<li>There is now a Concept Class for supplier information whose
|
|
|
|
|
|
relationships can be found in CONCEPT_ RELATIONSHIP with a
|
|
|
|
|
|
relationship_id of ‘Has supplier’ and ‘Supplier of’</li>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</ul>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
<div id="mapping" class="section level2">
|
|
|
|
|
|
<h2><strong>Mapping</strong></h2>
|
|
|
|
|
|
<div id="representing-content-as-concepts" class="section level3">
|
|
|
|
|
|
<h3>Representing content as Concepts</h3>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>In CDM data tables the meaning of the content of each record is
|
|
|
|
|
|
represented using Concepts. Concepts are stored with their CONCEPT_ID as
|
|
|
|
|
|
foreign keys to the CONCEPT table in the Standardized Vocabularies,
|
|
|
|
|
|
which contains Concepts necessary to describe the healthcare experience
|
|
|
|
|
|
of a patient. If a Standard Concept does not exist or cannot be
|
|
|
|
|
|
identified, the Concept with the CONCEPT_ID 0 is used, representing a
|
|
|
|
|
|
non-existing or un-mappable concept.</p>
|
|
|
|
|
|
<p>Records in the CONCEPT table contain all the detailed information
|
|
|
|
|
|
about it (name, domain, class etc.). Concepts, Concept Relationships and
|
|
|
|
|
|
other information relating to Concepts is contained in the tables of the
|
|
|
|
|
|
Standardized Vocabularies.</p>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</div>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<div id="concept-ids-and-source-values" class="section level3">
|
|
|
|
|
|
<h3>Concept IDs and Source Values</h3>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Many tables contain equivalent information multiple times: As a
|
|
|
|
|
|
Source Value, a Source Concept and as a Standard Concept.</p>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Source Values contain the codes from public code systems such as
|
|
|
|
|
|
ICD-9-CM, NDC, CPT-4 etc. or locally controlled vocabularies (such as F
|
|
|
|
|
|
for female and M for male) copied from the source data. Source Values
|
|
|
|
|
|
are stored in the *_SOURCE_VALUE fields in the data tables.</li>
|
|
|
|
|
|
<li>Concepts are CDM-specific entities that represent the meaning of a
|
|
|
|
|
|
clinical fact. Most concepts are based on code systems used in
|
|
|
|
|
|
healthcare (called Source Concepts), while others were created de-novo
|
|
|
|
|
|
(CONCEPT_CODE = ‘OMOP generated’). Concepts have unique IDs across all
|
|
|
|
|
|
domains.</li>
|
|
|
|
|
|
<li>Source Concepts are the concepts that represent the code used in the
|
|
|
|
|
|
source. Source Concepts are only used for common healthcare code
|
|
|
|
|
|
systems, not for OMOP-generated Concepts. Source Concepts are stored in
|
|
|
|
|
|
the *_SOURCE_CONCEPT_ID field in the data tables.</li>
|
|
|
|
|
|
<li>Standard Concepts are those concepts that are used to define the
|
|
|
|
|
|
unique meaning of a clinical entity. For each entity there is one
|
|
|
|
|
|
Standard Concept. Standard Concepts are typically drawn from existing
|
|
|
|
|
|
public vocabulary sources. Concepts that have the equivalent meaning to
|
|
|
|
|
|
a Standard Concept are mapped to the Standard Concept. Standard Concepts
|
|
|
|
|
|
are referred to in the <entity>_CONCEPT_ID field of the data
|
|
|
|
|
|
tables.</li>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Source Values are only provided for convenience and quality assurance
|
|
|
|
|
|
(QA) purposes. Source Values and Source Concepts are optional, while
|
|
|
|
|
|
Standard Concepts are mandatory. Source Values may contain information
|
|
|
|
|
|
that is only meaningful in the context of a specific data source.</p>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</div>
|
2021-09-22 19:39:44 +00:00
|
|
|
|
<div id="type-concepts" class="section level3">
|
|
|
|
|
|
<h3>Type Concepts</h3>
|
|
|
|
|
|
<p><em>By Mik Kallfelz and Dmitry Dymshyts</em></p>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Type Concepts (ending in _TYPE_CONCEPT_ID) are present in many
|
|
|
|
|
|
tables. They are special Concepts with the purpose of indicating from
|
|
|
|
|
|
where the data are derived in the source. For example, the Type Concept
|
|
|
|
|
|
field can be used to distinguish a DRUG_EXPOSURE record that is derived
|
|
|
|
|
|
from a pharmacy-dispensing claim from one indicative of a prescription
|
|
|
|
|
|
written in an electronic health record (EHR).</p>
|
2021-09-22 19:39:44 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Type concepts help determining the provenance of a record in the
|
|
|
|
|
|
OMOP CDM. Many tables hold a specific _type_concept_id field for which
|
|
|
|
|
|
<a
|
|
|
|
|
|
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=">valid
|
|
|
|
|
|
concepts</a> can be used to indicate a particular source of that record.
|
|
|
|
|
|
For a condition it can be helpful to know, if it was derived from an EHR
|
|
|
|
|
|
system or insurance claims. For a drug exposure it should be very useful
|
|
|
|
|
|
to distinguish between prescriptions and actual administrations.</li>
|
|
|
|
|
|
<li>In respect to the target table, matching type concepts should be
|
|
|
|
|
|
chosen during the ETL step while processing sources. There are various
|
|
|
|
|
|
representations in the list of type concepts of which some are quite
|
|
|
|
|
|
specific for one table and others can be applied for many tables /
|
|
|
|
|
|
domains, as they are quite generic. There is however no plausibility
|
|
|
|
|
|
check or dependency between type concepts and tables which means they
|
|
|
|
|
|
have to be chosen correctly.</li>
|
|
|
|
|
|
<li>There is now one specific <a
|
|
|
|
|
|
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary</a>
|
|
|
|
|
|
for type concepts which replaced a number of previously existing tables.
|
|
|
|
|
|
For example, where previously there was a dedicated vocabulary for Drug
|
|
|
|
|
|
Type Concepts, now we would choose the respective ones from the overall
|
|
|
|
|
|
vocabulary (and ignore some of the old ones):</li>
|
2021-09-22 19:39:44 +00:00
|
|
|
|
</ul>
|
|
|
|
|
|
<table>
|
|
|
|
|
|
<colgroup>
|
|
|
|
|
|
<col width="64%" />
|
|
|
|
|
|
<col width="35%" />
|
|
|
|
|
|
</colgroup>
|
|
|
|
|
|
<thead>
|
|
|
|
|
|
<tr class="header">
|
|
|
|
|
|
<th>Drug Type</th>
|
|
|
|
|
|
<th>Type Concept</th>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
</thead>
|
|
|
|
|
|
<tbody>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td>Inpatient administration</td>
|
|
|
|
|
|
<td>EHR administration record</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td>Physician administered drug (identified from EHR problem list)</td>
|
|
|
|
|
|
<td>EHR administration record</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td>Physician administered drug (identified from referral record)</td>
|
|
|
|
|
|
<td>EHR administration record</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td>Physician administered drug (identified from EHR observation)</td>
|
|
|
|
|
|
<td>EHR administration record</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td>Physician administered drug (identified from EHR order)</td>
|
|
|
|
|
|
<td>EHR administration record</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td>Prescription dispensed in pharmacy</td>
|
|
|
|
|
|
<td>EHR dispensing record</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td>Dispensed in Outpatient office</td>
|
|
|
|
|
|
<td>EHR dispensing record</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td>Medication list entry</td>
|
|
|
|
|
|
<td>EHR medication list</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td>Prescription written</td>
|
|
|
|
|
|
<td>EHR prescription</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td></td>
|
|
|
|
|
|
<td>EHR prescription issue record</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td>Prescription dispensed through mail order</td>
|
|
|
|
|
|
<td>Mail order record</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td>NLP derived</td>
|
|
|
|
|
|
<td>NLP</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td>Patient Self-Reported Medication</td>
|
|
|
|
|
|
<td>Patient self-report</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td>Physician administered drug (identified as procedure)</td>
|
|
|
|
|
|
<td>Pharmacy claim</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td>Drug era - 0 days persistence window</td>
|
|
|
|
|
|
<td></td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td>Drug era - 30 days persistence window</td>
|
|
|
|
|
|
<td></td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td>Randomized Drug</td>
|
|
|
|
|
|
<td></td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
</tbody>
|
|
|
|
|
|
</table>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</div>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<div id="time-span-of-available-data" class="section level3">
|
|
|
|
|
|
<h3>Time span of available data</h3>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Data tables for clinical data contain a datetime stamp (ending in
|
|
|
|
|
|
_DATETIME, _START_DATETIME or _END_DATETIME), indicating when that
|
|
|
|
|
|
clinical event occurred. As a rule, no record can be outside of a valid
|
|
|
|
|
|
OBSERVATION_PERIOD time period. Clinical information that relates to
|
|
|
|
|
|
events that happened prior to the first OBSERVATION_PERIOD will be
|
|
|
|
|
|
captured as a record in the OBSERVATION table as ‘Medical history’
|
|
|
|
|
|
(CONCEPT_ID = 43054928), with the OBSERVATION_DATETIME set to the first
|
|
|
|
|
|
OBSERVATION_PERIOD_START_DATE of that patient, and the
|
|
|
|
|
|
VALUE_AS_CONCEPT_ID set to the corresponding CONCEPT_ID for the
|
|
|
|
|
|
condition/drug/procedure that occurred in the past. No data occurring
|
|
|
|
|
|
after the last OBSERVATION_PERIOD_END_DATE can be valid records in the
|
|
|
|
|
|
CDM. * When mapping source data to the CDM, if time is unknown the
|
|
|
|
|
|
default time of 00:00:00 should be chosen.</p>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</div>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<div id="source-values-source-concept-ids-and-standard-concept-ids"
|
|
|
|
|
|
class="section level3">
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<h3>Source Values, Source Concept Ids, and Standard Concept Ids</h3>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Each table contains fields for Source Values, Source Concept Ids, and
|
|
|
|
|
|
Standard Concept Ids.</p>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Source Values are fields to maintain the verbatim information from
|
|
|
|
|
|
the source database, stored as unstructured text, and are generally not
|
|
|
|
|
|
to be used by any standardized analytics. There is no standardization
|
|
|
|
|
|
for these fields and these columns can be used as the local CDM builders
|
|
|
|
|
|
see fit. A typical example would be an ICD-9 code without the decimal
|
|
|
|
|
|
from an administrative claim as condition_source_value = ‘78702’ which
|
|
|
|
|
|
is how it appeared in the source.</li>
|
|
|
|
|
|
<li>Source Concept Ids provide a repeatable representation of the source
|
|
|
|
|
|
concept, when the source data are drawn from a commonly-used,
|
|
|
|
|
|
internationally-recognized vocabulary that has been distributed with the
|
|
|
|
|
|
OMOP Common Data Model. Specific use cases where source
|
|
|
|
|
|
vocabulary-specific analytics are required can be accommodated by the
|
|
|
|
|
|
use of the *_SOURCE_CONCEPT_ID fields, but these are generally not
|
|
|
|
|
|
applicable across disparate data sources. The standard *_CONCEPT_ID
|
|
|
|
|
|
fields are <strong>strongly suggested</strong> to be used in all
|
|
|
|
|
|
standardized analytics, as specific vocabularies have been established
|
|
|
|
|
|
within each data domain to facilitate standardization of both structure
|
|
|
|
|
|
and content within the OMOP Common Data Model.</li>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>The following provide conventions for processing source data using
|
|
|
|
|
|
these three fields in each domain:</p>
|
|
|
|
|
|
<p>When processing data where the source value is either free text or a
|
|
|
|
|
|
reference to a coding scheme that is not contained within the
|
|
|
|
|
|
Standardized Vocabularies:</p>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Map all Source Values to the corresponding Standard CONCEPT_IDs.
|
|
|
|
|
|
Store the CONCEPT_IDs in the TARGET_CONCEPT_ID field of the
|
|
|
|
|
|
SOURCE_TO_CONCEPT_MAP table.
|
2019-08-28 15:02:47 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>If a CONCEPT_ID is not available for the source code, the
|
|
|
|
|
|
TARGET_CONCEPT_ID field is set to 0.</li>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</ul></li>
|
|
|
|
|
|
</ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>When processing your data where Source Value is a reference to a
|
|
|
|
|
|
coding scheme contained within the Standardized Vocabularies:</p>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Find all CONCEPT_IDs in the Source Vocabulary that correspond to
|
|
|
|
|
|
your Source Values. Store the result in the SOURCE_CONCEPT_ID field.
|
2019-08-28 15:02:47 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>If the source code follows the same formatting as the distributed
|
|
|
|
|
|
vocabulary, the mapping can be directly obtained from the CONCEPT table
|
|
|
|
|
|
using the CONCEPT_CODE field.</li>
|
|
|
|
|
|
<li>If the source code uses alternative formatting (ex. format has
|
|
|
|
|
|
removed decimal point from ICD-9 codes), you will need to perform the
|
|
|
|
|
|
formatting transformation within the ETL. In this case, you may wish to
|
|
|
|
|
|
store the mappings from original codes to SOURCE_CONCEPT_IDs in the
|
|
|
|
|
|
SOURCE_TO_CONCEPT_MAP table.</li>
|
|
|
|
|
|
<li>If the source code is not found in a vocabulary, the
|
|
|
|
|
|
SOURCE_CONCEPT_ID field is set to 0</li>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</ul></li>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Use the CONCEPT_RELATIONSHIP table to identify the Standard
|
|
|
|
|
|
CONCEPT_ID that corresponds to the SOURCE_CONCEPT_ID in the domain.
|
2019-08-28 15:02:47 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Each SOURCE_CONCEPT_ID can have 1 or more Standard CONCEPT_IDs
|
|
|
|
|
|
mapped to it. Each Standard CONCEPT_ID belongs to only one primary
|
|
|
|
|
|
domain but when a source CONCEPT_ID maps to multiple Standard
|
|
|
|
|
|
CONCEPT_IDs, it is possible for that SOURCE_CONCEPT_ID to result in
|
|
|
|
|
|
records being produced across multiple domains. For example, ICD-10-CM
|
|
|
|
|
|
code Z34.00 ‘Encounter for supervision of normal first pregnancy,
|
|
|
|
|
|
unspecified trimester’ will be mapped to the SNOMED concept ‘Routine
|
|
|
|
|
|
antenatal care’ in the procedure domain and the concept in the condition
|
|
|
|
|
|
domain ‘Primagravida’. It is also possible for one SOURCE_CONCEPT_ID to
|
|
|
|
|
|
map to multiple Standard CONCEPT_IDs within the same domain. For
|
|
|
|
|
|
example, ICD-9-CM code 070.43 ‘Hepatitis E with hepatic coma’ maps to
|
|
|
|
|
|
the SNOMED concept for ‘Acute hepatitis E’ and a second SNOMED concept
|
|
|
|
|
|
for ‘Hepatic coma’, in which case multiple CONDITION_OCCURRENCE records
|
|
|
|
|
|
will be generated for the one source value record.</li>
|
|
|
|
|
|
<li>If the SOURCE_CONCEPT_ID is not mappable to any Standard CONCEPT_ID,
|
|
|
|
|
|
the <entity>_CONCEPT_ID field is set to 0.</li>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</ul></li>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>Write the data record into the table(s) corresponding to the domain
|
|
|
|
|
|
of the Standard CONCEPT_ID(s).
|
2019-08-28 15:02:47 +00:00
|
|
|
|
<ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<li>If the Source Value has a SOURCE_CONCEPT_ID but the
|
|
|
|
|
|
SOURCE_CONCEPT_ID is not mapped to a Standard CONCEPT_ID, then the
|
|
|
|
|
|
domain for the data record, and hence it’s table location, is determined
|
|
|
|
|
|
by the DOMAIN_ID field of the CONCEPT record the SOURCE_CONCEPT_ID
|
|
|
|
|
|
refers to. The Standard <entity>_CONCEPT_ID is set to 0.</li>
|
|
|
|
|
|
<li>If the Source Value cannot be mapped to a SOURCE_CONCEPT_ID or
|
|
|
|
|
|
Standard CONCEPT_ID, then direct the data record to the most appropriate
|
|
|
|
|
|
CDM domain based on your local knowledge of the intent of the source
|
|
|
|
|
|
data and associated value. For example, if the un-mappable Source Value
|
|
|
|
|
|
came from a ‘diagnosis’ table then, in the absence of other information,
|
|
|
|
|
|
you may choose to record that fact in the CONDITION_OCCURRENCE
|
|
|
|
|
|
table.</li>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</ul></li>
|
|
|
|
|
|
</ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>Each Standard CONCEPT_ID field has a set of allowable CONCEPT_ID
|
|
|
|
|
|
values. The allowable values are defined by the domain of the concepts.
|
|
|
|
|
|
For example, there is a domain concept of ‘Gender’, for which there are
|
|
|
|
|
|
only two allowable standard concepts of practical use (8507 - ‘Male’,
|
|
|
|
|
|
8532- ‘Female’) and one allowable generic concept to represent a
|
|
|
|
|
|
standard notion of ‘no information’ (concept_id = 0). This ‘no
|
|
|
|
|
|
information’ concept should be used when there is no mapping to a
|
|
|
|
|
|
standard concept available or if there is no information available for
|
|
|
|
|
|
that field. The exceptions are MEASUREMENT.VALUE_AS_CONCEPT_ID,
|
|
|
|
|
|
OBSERVATION.VALUE_AS_CONCEPT_ID, MEASUREMENT.UNIT_CONCEPT_ID,
|
|
|
|
|
|
OBSERVATION.UNIT_CONCEPT_ID, MEASUREMENT.OPERATOR_CONCEPT_ID, and
|
|
|
|
|
|
OBSERVATION.MODIFIER_CONCEPT_ID, which can be NULL if the data do not
|
|
|
|
|
|
contain the information (<a
|
|
|
|
|
|
href="https://github.com/OHDSI/Themis/issues/11">THEMIS issue
|
|
|
|
|
|
#11</a>).</p>
|
|
|
|
|
|
<p>There is no constraint on allowed CONCEPT_IDs within the
|
|
|
|
|
|
SOURCE_CONCEPT_ID fields.</p>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</div>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
<div id="custom-source_to_concept_map" class="section level3">
|
|
|
|
|
|
<h3>Custom SOURCE_TO_CONCEPT_MAP</h3>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>When the source data uses coding systems that are not currently in
|
|
|
|
|
|
the Standardized Vocabularies (e.g. ICPC codes for diagnoses), the
|
|
|
|
|
|
convention is to store the mapping of such source codes to Standard
|
|
|
|
|
|
Concepts in the SOURCE_TO_CONCEPT_MAP table. The codes used in the data
|
|
|
|
|
|
source can be recorded in the SOURCE_VALUE fields, but no
|
|
|
|
|
|
SOURCE_CONCEPT_ID will be available.</p>
|
|
|
|
|
|
<p>Custom source codes are not allowed to map to Standard Concepts that
|
|
|
|
|
|
are marked as invalid.</p>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</div>
|
2020-10-06 15:11:13 +00:00
|
|
|
|
</div>
|
|
|
|
|
|
</div>
|
2019-08-28 15:02:47 +00:00
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</div>
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</div>
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</div>
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<script>
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// add bootstrap table styles to pandoc tables
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function bootstrapStylePandocTables() {
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2021-01-06 15:52:57 +00:00
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$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
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2019-08-28 15:02:47 +00:00
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}
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$(document).ready(function () {
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bootstrapStylePandocTables();
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});
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</script>
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2020-04-27 20:35:41 +00:00
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<!-- tabsets -->
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<script>
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$(document).ready(function () {
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window.buildTabsets("TOC");
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});
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$(document).ready(function () {
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$('.tabset-dropdown > .nav-tabs > li').click(function () {
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2022-01-13 18:59:03 +00:00
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$(this).parent().toggleClass('nav-tabs-open');
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2020-04-27 20:35:41 +00:00
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});
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});
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</script>
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<!-- code folding -->
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<script>
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$(document).ready(function () {
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2022-01-13 18:59:03 +00:00
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// temporarily add toc-ignore selector to headers for the consistency with Pandoc
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$('.unlisted.unnumbered').addClass('toc-ignore')
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2020-04-27 20:35:41 +00:00
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// move toc-ignore selectors from section div to header
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$('div.section.toc-ignore')
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.removeClass('toc-ignore')
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.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
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// establish options
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var options = {
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selectors: "h1,h2,h3",
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theme: "bootstrap3",
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context: '.toc-content',
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hashGenerator: function (text) {
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2021-01-06 15:52:57 +00:00
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return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
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2020-04-27 20:35:41 +00:00
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},
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ignoreSelector: ".toc-ignore",
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scrollTo: 0
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};
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options.showAndHide = true;
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options.smoothScroll = true;
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// tocify
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var toc = $("#TOC").tocify(options).data("toc-tocify");
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});
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</script>
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2019-08-28 15:02:47 +00:00
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<!-- dynamically load mathjax for compatibility with self-contained -->
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<script>
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(function () {
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var script = document.createElement("script");
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script.type = "text/javascript";
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script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
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document.getElementsByTagName("head")[0].appendChild(script);
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})();
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</script>
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</body>
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</html>
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