2021-09-22 19:39:44 +00:00
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<!DOCTYPE html>
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<html>
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<head>
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<meta charset="utf-8" />
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<meta name="generator" content="pandoc" />
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<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
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<title>Indices, Primary Keys and Foreign Key Constraints</title>
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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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2021-09-22 19:39:44 +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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2021-09-22 19:39:44 +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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2021-09-22 19:39:44 +00:00
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<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
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<style type="text/css">
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code{white-space: pre-wrap;}
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span.smallcaps{font-variant: small-caps;}
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span.underline{text-decoration: underline;}
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div.column{display: inline-block; vertical-align: top; width: 50%;}
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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ul.task-list{list-style: none;}
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</style>
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<style type="text/css">code{white-space: pre;}</style>
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<script type="text/javascript">
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if (window.hljs) {
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hljs.configure({languages: []});
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hljs.initHighlightingOnLoad();
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if (document.readyState && document.readyState === "complete") {
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window.setTimeout(function() { hljs.initHighlighting(); }, 0);
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}
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}
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</script>
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2022-07-27 01:48:28 +00:00
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2021-09-22 19:39:44 +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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2021-09-22 19:39:44 +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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2021-09-22 19:39:44 +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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2021-09-22 19:39:44 +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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2021-09-22 19:39:44 +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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2021-09-22 19:39:44 +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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2021-09-22 19:39:44 +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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2021-09-22 19:39:44 +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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<a href="drug_dose.html">Calculate Drug Dose</a>
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<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
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2021-09-22 19:39:44 +00:00
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</div><!--/.container -->
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</div><!--/.navbar -->
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2022-01-13 18:59:03 +00:00
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<div id="header">
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2023-02-08 20:04:22 +00:00
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<h1 class="title toc-ignore">Indices, Primary Keys and Foreign Key
|
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Constraints</h1>
|
2021-09-22 19:39:44 +00:00
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</div>
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<div id="overview" class="section level2">
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<h2>Overview</h2>
|
2023-02-08 20:04:22 +00:00
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<p>Database indices improve the performance of queries against a
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database by organizing the data in a way that increase query
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execution.</p>
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<p>This article was written to provide guidance on the setting of
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indices, primary and foreign keys for data that has been transformed
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into the Observational Medical Outcome Partnership (OMOP) Common Data
|
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Model (CDM). The community that supports the design and development of
|
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the OHDSI/CommonDataModel Github repository is a diverse collaborative
|
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of healthcare and technical profesisonals whom have limited data base
|
2024-03-28 19:09:22 +00:00
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administrative (DBA) experience. As a result, the comments below should
|
2023-02-08 20:04:22 +00:00
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be interpreted as suggestions and recommendations to help increase
|
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performance. Your teams needs may call for a modified configuration.</p>
|
2021-09-22 19:39:44 +00:00
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</div>
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<div id="general-recommendations" class="section level2">
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<h2>General Recommendations</h2>
|
2023-02-08 20:04:22 +00:00
|
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|
|
<p>Should your database of choice support indexing, the OMOP CDM Working
|
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|
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|
Group recommends</p>
|
2021-09-22 19:39:44 +00:00
|
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<ul>
|
2023-02-08 20:04:22 +00:00
|
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<li>Indexing on all columns containing an “_id”
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(e.g. condition_occurrence_id, drug_exposure_id, measurement_id,
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procedure_occurrence_id, etc.)</li>
|
2021-09-22 19:39:44 +00:00
|
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<li>Indexing on primary and foreign keys</li>
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</ul>
|
2023-02-08 20:04:22 +00:00
|
|
|
|
<p>For all databases, regardless of custom indice support, primary and
|
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foreign keys should be set. This is a step towards ensuring data
|
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integrity. Information on what table level attributes should be set as
|
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|
primary and foreign keys can be found within the *_Field_Level.csv
|
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|
file(s) located in the <a
|
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|
href="https://github.com/OHDSI/CommonDataModel/tree/v5.4/inst/csv">INST/CSV
|
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|
directory</a></p>
|
2021-09-22 19:39:44 +00:00
|
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|
</div>
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|
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|
|
<div id="database-support" class="section level2">
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|
<h2>Database support</h2>
|
2023-02-08 20:04:22 +00:00
|
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|
|
<p>The OHDSI/CommonDataModel package leverages OHDSI/SQLRender and as a
|
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|
result is only capable of supporting sources that are supported by
|
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|
OHDSI/SQLRender. The following databases are currently supported.</p>
|
2021-09-22 19:39:44 +00:00
|
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|
<div id="microsoft-sql-server" class="section level3">
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<h3>Microsoft SQL Server</h3>
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</div>
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<div id="oracle" class="section level3">
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<h3>Oracle</h3>
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</div>
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<div id="postgresql" class="section level3">
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<h3>PostgreSQL</h3>
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</div>
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<div id="amazon-redshift" class="section level3">
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<h3>Amazon Redshift</h3>
|
2023-02-08 20:04:22 +00:00
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<p>On AWS Redshift it is important to ensure that your data is properly
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distributed and sorted across nodes. Compression on certain columns may
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also help. The designed DDL does set DISTKEYS in an effort to optimize
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performance. This configuration can be seen within the <a
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href="https://github.com/OHDSI/CommonDataModel/blob/v5.4/ddl/5.4/redshift/OMOPCDM_redshift_5.4_ddl.sql">Redshift-specific
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DDL</a>.</p>
|
2021-09-22 19:39:44 +00:00
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</div>
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<div id="impala" class="section level3">
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<h3>Impala</h3>
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</div>
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<div id="ibm-netezza" class="section level3">
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<h3>IBM Netezza</h3>
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</div>
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<div id="google-bigquery" class="section level3">
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<h3>Google BigQuery</h3>
|
2023-02-08 20:04:22 +00:00
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<p>Google BigQuery does not require manual optimization and/or sizing.
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Google BigQuery does massive parallel full table scans and intensive
|
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caching, all under the hood. <a
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href="https://forums.ohdsi.org/t/iso-best-practices-of-cdm-indexing/10939/2">Reference</a></p>
|
2021-09-22 19:39:44 +00:00
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</div>
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<div id="microsoft-parallel-data-warehouse-pdw" class="section level3">
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<h3>Microsoft Parallel Data Warehouse (PDW)</h3>
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</div>
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<div id="sqlite" class="section level3">
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<h3>SQLite</h3>
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</div>
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<div id="databricks" class="section level3">
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<h3>Databricks</h3>
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</div>
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</div>
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<div id="references" class="section level2">
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<h2>References</h2>
|
2023-02-08 20:04:22 +00:00
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<p><a
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href="https://forums.ohdsi.org/t/iso-best-practices-of-cdm-indexing/10939/2">ISO
|
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|
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|
Best Practices of CDM Indexing</a></p>
|
2021-09-22 19:39:44 +00:00
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</div>
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</div>
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</div>
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</div>
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<script>
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bootstrapStylePandocTables();
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</script>
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<!-- tabsets -->
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<script>
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$(document).ready(function () {
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$('.tabset-dropdown > .nav-tabs > li').click(function () {
|
2022-01-13 18:59:03 +00:00
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$(this).parent().toggleClass('nav-tabs-open');
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2021-09-22 19:39:44 +00:00
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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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2021-09-22 19:39:44 +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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// establish options
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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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