1463 lines
35 KiB
HTML
1463 lines
35 KiB
HTML
|
<!DOCTYPE html>
|
|||
|
|
|
|||
|
|
<html>
|
|||
|
|
|
|||
|
|
<head>
|
|||
|
|
|
|||
|
|
<meta charset="utf-8" />
|
|||
|
|
<meta name="generator" content="pandoc" />
|
|||
|
|
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<title>OMOP CDM v5.4 Detailed Tooling Support</title>
|
|||
|
|
|
|||
|
|
<script src="site_libs/header-attrs-2.17/header-attrs.js"></script>
|
|||
|
|
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
|
|||
|
|
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
|||
|
|
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
|
|||
|
|
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
|
|||
|
|
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
|
|||
|
|
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
|
|||
|
|
<style>h1 {font-size: 34px;}
|
|||
|
|
h1.title {font-size: 38px;}
|
|||
|
|
h2 {font-size: 30px;}
|
|||
|
|
h3 {font-size: 24px;}
|
|||
|
|
h4 {font-size: 18px;}
|
|||
|
|
h5 {font-size: 16px;}
|
|||
|
|
h6 {font-size: 12px;}
|
|||
|
|
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
|
|||
|
|
pre:not([class]) { background-color: white }</style>
|
|||
|
|
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
|
|||
|
|
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
|
|||
|
|
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
|
|||
|
|
<script src="site_libs/navigation-1.1/tabsets.js"></script>
|
|||
|
|
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
|
|||
|
|
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
|
|||
|
|
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
|
|||
|
|
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
|
|||
|
|
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
|
|||
|
|
|
|||
|
|
<style type="text/css">
|
|||
|
|
code{white-space: pre-wrap;}
|
|||
|
|
span.smallcaps{font-variant: small-caps;}
|
|||
|
|
span.underline{text-decoration: underline;}
|
|||
|
|
div.column{display: inline-block; vertical-align: top; width: 50%;}
|
|||
|
|
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
|
|||
|
|
ul.task-list{list-style: none;}
|
|||
|
|
</style>
|
|||
|
|
|
|||
|
|
<style type="text/css">code{white-space: pre;}</style>
|
|||
|
|
<script type="text/javascript">
|
|||
|
|
if (window.hljs) {
|
|||
|
|
hljs.configure({languages: []});
|
|||
|
|
hljs.initHighlightingOnLoad();
|
|||
|
|
if (document.readyState && document.readyState === "complete") {
|
|||
|
|
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<link rel="stylesheet" href="style.css" type="text/css" />
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<style type = "text/css">
|
|||
|
|
.main-container {
|
|||
|
|
max-width: 940px;
|
|||
|
|
margin-left: auto;
|
|||
|
|
margin-right: auto;
|
|||
|
|
}
|
|||
|
|
img {
|
|||
|
|
max-width:100%;
|
|||
|
|
}
|
|||
|
|
.tabbed-pane {
|
|||
|
|
padding-top: 12px;
|
|||
|
|
}
|
|||
|
|
.html-widget {
|
|||
|
|
margin-bottom: 20px;
|
|||
|
|
}
|
|||
|
|
button.code-folding-btn:focus {
|
|||
|
|
outline: none;
|
|||
|
|
}
|
|||
|
|
summary {
|
|||
|
|
display: list-item;
|
|||
|
|
}
|
|||
|
|
details > summary > p:only-child {
|
|||
|
|
display: inline;
|
|||
|
|
}
|
|||
|
|
pre code {
|
|||
|
|
padding: 0;
|
|||
|
|
}
|
|||
|
|
</style>
|
|||
|
|
|
|||
|
|
|
|||
|
|
<style type="text/css">
|
|||
|
|
.dropdown-submenu {
|
|||
|
|
position: relative;
|
|||
|
|
}
|
|||
|
|
.dropdown-submenu>.dropdown-menu {
|
|||
|
|
top: 0;
|
|||
|
|
left: 100%;
|
|||
|
|
margin-top: -6px;
|
|||
|
|
margin-left: -1px;
|
|||
|
|
border-radius: 0 6px 6px 6px;
|
|||
|
|
}
|
|||
|
|
.dropdown-submenu:hover>.dropdown-menu {
|
|||
|
|
display: block;
|
|||
|
|
}
|
|||
|
|
.dropdown-submenu>a:after {
|
|||
|
|
display: block;
|
|||
|
|
content: " ";
|
|||
|
|
float: right;
|
|||
|
|
width: 0;
|
|||
|
|
height: 0;
|
|||
|
|
border-color: transparent;
|
|||
|
|
border-style: solid;
|
|||
|
|
border-width: 5px 0 5px 5px;
|
|||
|
|
border-left-color: #cccccc;
|
|||
|
|
margin-top: 5px;
|
|||
|
|
margin-right: -10px;
|
|||
|
|
}
|
|||
|
|
.dropdown-submenu:hover>a:after {
|
|||
|
|
border-left-color: #adb5bd;
|
|||
|
|
}
|
|||
|
|
.dropdown-submenu.pull-left {
|
|||
|
|
float: none;
|
|||
|
|
}
|
|||
|
|
.dropdown-submenu.pull-left>.dropdown-menu {
|
|||
|
|
left: -100%;
|
|||
|
|
margin-left: 10px;
|
|||
|
|
border-radius: 6px 0 6px 6px;
|
|||
|
|
}
|
|||
|
|
</style>
|
|||
|
|
|
|||
|
|
<script type="text/javascript">
|
|||
|
|
// manage active state of menu based on current page
|
|||
|
|
$(document).ready(function () {
|
|||
|
|
// active menu anchor
|
|||
|
|
href = window.location.pathname
|
|||
|
|
href = href.substr(href.lastIndexOf('/') + 1)
|
|||
|
|
if (href === "")
|
|||
|
|
href = "index.html";
|
|||
|
|
var menuAnchor = $('a[href="' + href + '"]');
|
|||
|
|
|
|||
|
|
// mark the anchor link active (and if it's in a dropdown, also mark that active)
|
|||
|
|
var dropdown = menuAnchor.closest('li.dropdown');
|
|||
|
|
if (window.bootstrap) { // Bootstrap 4+
|
|||
|
|
menuAnchor.addClass('active');
|
|||
|
|
dropdown.find('> .dropdown-toggle').addClass('active');
|
|||
|
|
} else { // Bootstrap 3
|
|||
|
|
menuAnchor.parent().addClass('active');
|
|||
|
|
dropdown.addClass('active');
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
// Navbar adjustments
|
|||
|
|
var navHeight = $(".navbar").first().height() + 15;
|
|||
|
|
var style = document.createElement('style');
|
|||
|
|
var pt = "padding-top: " + navHeight + "px; ";
|
|||
|
|
var mt = "margin-top: -" + navHeight + "px; ";
|
|||
|
|
var css = "";
|
|||
|
|
// offset scroll position for anchor links (for fixed navbar)
|
|||
|
|
for (var i = 1; i <= 6; i++) {
|
|||
|
|
css += ".section h" + i + "{ " + pt + mt + "}\n";
|
|||
|
|
}
|
|||
|
|
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
|
|||
|
|
document.head.appendChild(style);
|
|||
|
|
});
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
<!-- tabsets -->
|
|||
|
|
|
|||
|
|
<style type="text/css">
|
|||
|
|
.tabset-dropdown > .nav-tabs {
|
|||
|
|
display: inline-table;
|
|||
|
|
max-height: 500px;
|
|||
|
|
min-height: 44px;
|
|||
|
|
overflow-y: auto;
|
|||
|
|
border: 1px solid #ddd;
|
|||
|
|
border-radius: 4px;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
|||
|
|
content: "\e259";
|
|||
|
|
font-family: 'Glyphicons Halflings';
|
|||
|
|
display: inline-block;
|
|||
|
|
padding: 10px;
|
|||
|
|
border-right: 1px solid #ddd;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
|
|||
|
|
content: "\e258";
|
|||
|
|
font-family: 'Glyphicons Halflings';
|
|||
|
|
border: none;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.tabset-dropdown > .nav-tabs > li.active {
|
|||
|
|
display: block;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.tabset-dropdown > .nav-tabs > li > a,
|
|||
|
|
.tabset-dropdown > .nav-tabs > li > a:focus,
|
|||
|
|
.tabset-dropdown > .nav-tabs > li > a:hover {
|
|||
|
|
border: none;
|
|||
|
|
display: inline-block;
|
|||
|
|
border-radius: 4px;
|
|||
|
|
background-color: transparent;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
|
|||
|
|
display: block;
|
|||
|
|
float: none;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.tabset-dropdown > .nav-tabs > li {
|
|||
|
|
display: none;
|
|||
|
|
}
|
|||
|
|
</style>
|
|||
|
|
|
|||
|
|
<!-- code folding -->
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<style type="text/css">
|
|||
|
|
|
|||
|
|
#TOC {
|
|||
|
|
margin: 25px 0px 20px 0px;
|
|||
|
|
}
|
|||
|
|
@media (max-width: 768px) {
|
|||
|
|
#TOC {
|
|||
|
|
position: relative;
|
|||
|
|
width: 100%;
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
@media print {
|
|||
|
|
.toc-content {
|
|||
|
|
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
|
|||
|
|
float: right;
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.toc-content {
|
|||
|
|
padding-left: 30px;
|
|||
|
|
padding-right: 40px;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
div.main-container {
|
|||
|
|
max-width: 1200px;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
div.tocify {
|
|||
|
|
width: 20%;
|
|||
|
|
max-width: 260px;
|
|||
|
|
max-height: 85%;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
@media (min-width: 768px) and (max-width: 991px) {
|
|||
|
|
div.tocify {
|
|||
|
|
width: 25%;
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
@media (max-width: 767px) {
|
|||
|
|
div.tocify {
|
|||
|
|
width: 100%;
|
|||
|
|
max-width: none;
|
|||
|
|
}
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.tocify ul, .tocify li {
|
|||
|
|
line-height: 20px;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.tocify-subheader .tocify-item {
|
|||
|
|
font-size: 0.90em;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
.tocify .list-group-item {
|
|||
|
|
border-radius: 0px;
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
|
|||
|
|
</style>
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
</head>
|
|||
|
|
|
|||
|
|
<body>
|
|||
|
|
|
|||
|
|
|
|||
|
|
<div class="container-fluid main-container">
|
|||
|
|
|
|||
|
|
|
|||
|
|
<!-- setup 3col/9col grid for toc_float and main content -->
|
|||
|
|
<div class="row">
|
|||
|
|
<div class="col-xs-12 col-sm-4 col-md-3">
|
|||
|
|
<div id="TOC" class="tocify">
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
|||
|
|
<div class="container">
|
|||
|
|
<div class="navbar-header">
|
|||
|
|
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
|
|||
|
|
<span class="icon-bar"></span>
|
|||
|
|
<span class="icon-bar"></span>
|
|||
|
|
<span class="icon-bar"></span>
|
|||
|
|
</button>
|
|||
|
|
<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
|
|||
|
|
</div>
|
|||
|
|
<div id="navbar" class="navbar-collapse collapse">
|
|||
|
|
<ul class="nav navbar-nav">
|
|||
|
|
<li>
|
|||
|
|
<a href="index.html">
|
|||
|
|
<span class="fa fa-house"></span>
|
|||
|
|
|
|||
|
|
</a>
|
|||
|
|
</li>
|
|||
|
|
<li class="dropdown">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
|||
|
|
<span class="fa fa-landmark"></span>
|
|||
|
|
|
|||
|
|
Background
|
|||
|
|
|
|||
|
|
<span class="caret"></span>
|
|||
|
|
</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="background.html">Model Background</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
<li class="dropdown">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
|||
|
|
<span class="fa fa-list-alt"></span>
|
|||
|
|
|
|||
|
|
Conventions
|
|||
|
|
|
|||
|
|
<span class="caret"></span>
|
|||
|
|
</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="dataModelConventions.html">General Conventions</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
<li class="dropdown">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
|||
|
|
<span class="fa fa-history"></span>
|
|||
|
|
|
|||
|
|
CDM Versions
|
|||
|
|
|
|||
|
|
<span class="caret"></span>
|
|||
|
|
</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="cdm30.html">CDM v3.0</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="cdm60.html">CDM v6.0</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="cdm53.html">CDM v5.3</a>
|
|||
|
|
</li>
|
|||
|
|
<li class="dropdown-submenu">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">NEW CDM v5.4</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="cdm54.html">CDM v5.4</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="cdm54erd.html">Entity Relationships</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="cdm54ToolingSupport.html">Detailed tooling support per CDM field</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
<li class="dropdown">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
|||
|
|
<span class="fa fa-plus-square"></span>
|
|||
|
|
|
|||
|
|
CDM Proposals
|
|||
|
|
|
|||
|
|
<span class="caret"></span>
|
|||
|
|
</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
|||
|
|
</li>
|
|||
|
|
<li class="dropdown-submenu">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Accepted</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
<li class="dropdown">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
|||
|
|
<span class="fa fa-question"></span>
|
|||
|
|
|
|||
|
|
How to
|
|||
|
|
|
|||
|
|
<span class="caret"></span>
|
|||
|
|
</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="download.html">Download the DDL</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="drug_dose.html">Calculate Drug Dose</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
<li class="dropdown">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
|||
|
|
<span class="fa fa-life-ring"></span>
|
|||
|
|
|
|||
|
|
Support
|
|||
|
|
|
|||
|
|
<span class="caret"></span>
|
|||
|
|
</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="faq.html">FAQ</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="sqlScripts.html">SQL Scripts</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="contribute.html">Ask a Question</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
<ul class="nav navbar-nav navbar-right">
|
|||
|
|
<li>
|
|||
|
|
<a href="https://github.com/OHDSI/CommonDataModel">
|
|||
|
|
<span class="fa fa-github"></span>
|
|||
|
|
|
|||
|
|
</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</div><!--/.nav-collapse -->
|
|||
|
|
</div><!--/.container -->
|
|||
|
|
</div><!--/.navbar -->
|
|||
|
|
|
|||
|
|
<div id="header">
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<h1 class="title toc-ignore"><strong>OMOP CDM v5.4 Detailed Tooling
|
|||
|
|
Support</strong></h1>
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
|
|||
|
|
<div id="introduction" class="section level1">
|
|||
|
|
<h1>Introduction</h1>
|
|||
|
|
<p>This tables below contain an overview of which standard OHDSI tools
|
|||
|
|
make use of which OMOP CDM fields. The goal is to inform ETL developers,
|
|||
|
|
tooling developers and CDM extensions.</p>
|
|||
|
|
<ul>
|
|||
|
|
<li>For ETL developers it helps to have guidance on which fieds to
|
|||
|
|
prioritise in the mapping. Most value will be gained from populating
|
|||
|
|
fields support across the OHDSI tooling.</li>
|
|||
|
|
<li>For OHDSI tooling developers, this page provides insight in the gaps
|
|||
|
|
of support and can drive future development efforts.</li>
|
|||
|
|
<li>For CDM extenstions, it helps to known what it means for an OMOP CDM
|
|||
|
|
table/field to be part of the standard. In other words: what OHDSI
|
|||
|
|
tooling do we at least expect to support the new extensions?</li>
|
|||
|
|
</ul>
|
|||
|
|
<p>Currently four OHDSI tools have been evaluated: DataQualityDashboard,
|
|||
|
|
Achilles, Atlas (Data Sources and Cohort creation) and Feature
|
|||
|
|
Extraction.</p>
|
|||
|
|
<div id="criteria" class="section level2">
|
|||
|
|
<h2>Criteria</h2>
|
|||
|
|
<table>
|
|||
|
|
<colgroup>
|
|||
|
|
<col width="33%" />
|
|||
|
|
<col width="33%" />
|
|||
|
|
<col width="33%" />
|
|||
|
|
</colgroup>
|
|||
|
|
<thead>
|
|||
|
|
<tr class="header">
|
|||
|
|
<th>Tool</th>
|
|||
|
|
<th>Supports CDM Field if</th>
|
|||
|
|
<th>Link to resource used</th>
|
|||
|
|
</tr>
|
|||
|
|
</thead>
|
|||
|
|
<tbody>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>DataQualityDashboard</td>
|
|||
|
|
<td>Part of Field Level checks</td>
|
|||
|
|
<td><a
|
|||
|
|
href="https://github.com/OHDSI/DataQualityDashboard/blob/main/inst/csv/OMOP_CDMv5.4_Field_Level.csv"
|
|||
|
|
class="uri">https://github.com/OHDSI/DataQualityDashboard/blob/main/inst/csv/OMOP_CDMv5.4_Field_Level.csv</a></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>Achilles</td>
|
|||
|
|
<td>Covered by at least one Achilles analysis</td>
|
|||
|
|
<td><a
|
|||
|
|
href="https://github.com/OHDSI/Achilles/blob/main/inst/csv/achilles/achilles_analysis_details.csv"
|
|||
|
|
class="uri">https://github.com/OHDSI/Achilles/blob/main/inst/csv/achilles/achilles_analysis_details.csv</a></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>Atlas Data Sources</td>
|
|||
|
|
<td>A statistic based on the field is shown in a ‘Data Sources’
|
|||
|
|
visualisation</td>
|
|||
|
|
<td><a href="https://atlas-demo.ohdsi.org/"
|
|||
|
|
class="uri">https://atlas-demo.ohdsi.org/</a></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>Atlas Cohort</td>
|
|||
|
|
<td>Used in te Atlas User Interface for cohort definition criteria
|
|||
|
|
(directly, or via ‘Add attribute’)</td>
|
|||
|
|
<td><a href="https://atlas-demo.ohdsi.org/"
|
|||
|
|
class="uri">https://atlas-demo.ohdsi.org/</a></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>Feature Extraction</td>
|
|||
|
|
<td>Used in one of the Feature Extraction analyses</td>
|
|||
|
|
<td><a
|
|||
|
|
href="https://github.com/OHDSI/FeatureExtraction/blob/main/inst/csv/"
|
|||
|
|
class="uri">https://github.com/OHDSI/FeatureExtraction/blob/main/inst/csv/</a></td>
|
|||
|
|
</tr>
|
|||
|
|
</tbody>
|
|||
|
|
</table>
|
|||
|
|
<p>General criteria: - ✅ if the field essential for OMOP CDM definition
|
|||
|
|
(Primary Key, Foreign Key) e.g. person_id not explicitly used, but
|
|||
|
|
essential. (if the PK is marked as False, it typically means the whole
|
|||
|
|
table is not used in the tool e.g. <code>_source_value</code> fields
|
|||
|
|
that are used for traceability in ETL) - ⚠️ if field is used by the
|
|||
|
|
tool, but not in a meaningful way. e.g. <code>provider_id</code> in
|
|||
|
|
Achilles only checked for a valid foreign key to the provider table.</p>
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
<div id="tooling-support-for-omop-fields" class="section level1">
|
|||
|
|
<h1>Tooling Support for OMOP fields</h1>
|
|||
|
|
<table>
|
|||
|
|
<colgroup>
|
|||
|
|
<col width="50%" />
|
|||
|
|
<col width="50%" />
|
|||
|
|
</colgroup>
|
|||
|
|
<thead>
|
|||
|
|
<tr class="header">
|
|||
|
|
<th><strong>Abbrevations</strong></th>
|
|||
|
|
<th> </th>
|
|||
|
|
</tr>
|
|||
|
|
</thead>
|
|||
|
|
<tbody>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td><strong>PK</strong></td>
|
|||
|
|
<td>Primary Key</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td><strong>SV</strong></td>
|
|||
|
|
<td>Source Value (for data quality / etl validation)</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td><strong>BC</strong></td>
|
|||
|
|
<td>Backwards Compatibility, to support CDM <v5.4</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td><strong>FC</strong></td>
|
|||
|
|
<td>Forwards Compatibility, to easy support for CDM v6 in the
|
|||
|
|
future.</td>
|
|||
|
|
</tr>
|
|||
|
|
</tbody>
|
|||
|
|
</table>
|
|||
|
|
<div id="person" class="section level2">
|
|||
|
|
<h2>Person</h2>
|
|||
|
|
<table>
|
|||
|
|
<colgroup>
|
|||
|
|
<col width="6%" />
|
|||
|
|
<col width="6%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="6%" />
|
|||
|
|
</colgroup>
|
|||
|
|
<thead>
|
|||
|
|
<tr class="header">
|
|||
|
|
<th>cdmTableName</th>
|
|||
|
|
<th>cdmFieldName</th>
|
|||
|
|
<th align="center">Special Fields</th>
|
|||
|
|
<th align="center">DQD (v1.0)</th>
|
|||
|
|
<th align="center">Achilles (v1.7)</th>
|
|||
|
|
<th align="center">Atlas Cohort (v2.10)</th>
|
|||
|
|
<th align="center">Atlas Cohort (v2.12)</th>
|
|||
|
|
<th align="center">Atlas Data Sources (v2.12)</th>
|
|||
|
|
<th align="center">Feature Extraction (v3.2)</th>
|
|||
|
|
<th>Comment</th>
|
|||
|
|
</tr>
|
|||
|
|
</thead>
|
|||
|
|
<tbody>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>person_id</td>
|
|||
|
|
<td align="center">PK</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>gender_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>year_of_birth</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>month_of_birth</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>day_of_birth</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>birth_datetime</td>
|
|||
|
|
<td align="center">FC</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>race_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>ethnicity_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>location_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">⚠️</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td>Achilles only does FK check</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>provider_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">⚠️</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td>Achilles only does FK check</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>care_site_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">⚠️</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td>Achilles only does FK check</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>person_source_value</td>
|
|||
|
|
<td align="center">SV</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>gender_source_value</td>
|
|||
|
|
<td align="center">SV</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>gender_source_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>race_source_value</td>
|
|||
|
|
<td align="center">SV</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>race_source_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>ethnicity_source_value</td>
|
|||
|
|
<td align="center">SV</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>PERSON</td>
|
|||
|
|
<td>ethnicity_source_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
</tbody>
|
|||
|
|
</table>
|
|||
|
|
</div>
|
|||
|
|
<div id="observation-period" class="section level2">
|
|||
|
|
<h2>Observation Period</h2>
|
|||
|
|
<table>
|
|||
|
|
<colgroup>
|
|||
|
|
<col width="6%" />
|
|||
|
|
<col width="6%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="6%" />
|
|||
|
|
</colgroup>
|
|||
|
|
<thead>
|
|||
|
|
<tr class="header">
|
|||
|
|
<th>cdmTableName</th>
|
|||
|
|
<th>cdmFieldName</th>
|
|||
|
|
<th align="center">Special Fields</th>
|
|||
|
|
<th align="center">DQD (v1.0)</th>
|
|||
|
|
<th align="center">Achilles (v1.7)</th>
|
|||
|
|
<th align="center">Atlas Cohort (v2.10)</th>
|
|||
|
|
<th align="center">Atlas Cohort (v2.12)</th>
|
|||
|
|
<th align="center">Atlas Data Sources (v2.12)</th>
|
|||
|
|
<th align="center">Feature Extraction (v3.2)</th>
|
|||
|
|
<th>Comment</th>
|
|||
|
|
</tr>
|
|||
|
|
</thead>
|
|||
|
|
<tbody>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>OBSERVATION_PERIOD</td>
|
|||
|
|
<td>observation_period_id</td>
|
|||
|
|
<td align="center">PK</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>OBSERVATION_PERIOD</td>
|
|||
|
|
<td>person_id</td>
|
|||
|
|
<td align="center">Pid</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>OBSERVATION_PERIOD</td>
|
|||
|
|
<td>observation_period_start_date</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>OBSERVATION_PERIOD</td>
|
|||
|
|
<td>observation_period_end_date</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>OBSERVATION_PERIOD</td>
|
|||
|
|
<td>period_type_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
</tbody>
|
|||
|
|
</table>
|
|||
|
|
</div>
|
|||
|
|
<div id="visit-occurrence" class="section level2">
|
|||
|
|
<h2>Visit Occurrence</h2>
|
|||
|
|
<table>
|
|||
|
|
<colgroup>
|
|||
|
|
<col width="6%" />
|
|||
|
|
<col width="6%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="6%" />
|
|||
|
|
</colgroup>
|
|||
|
|
<thead>
|
|||
|
|
<tr class="header">
|
|||
|
|
<th>cdmTableName</th>
|
|||
|
|
<th>cdmFieldName</th>
|
|||
|
|
<th align="center">Special Fields</th>
|
|||
|
|
<th align="center">DQD (v1.0)</th>
|
|||
|
|
<th align="center">Achilles (v1.7)</th>
|
|||
|
|
<th align="center">Atlas Cohort (v2.10)</th>
|
|||
|
|
<th align="center">Atlas Cohort (v2.12)</th>
|
|||
|
|
<th align="center">Atlas Data Sources (v2.12)</th>
|
|||
|
|
<th align="center">Feature Extraction (v3.2)</th>
|
|||
|
|
<th>Comment</th>
|
|||
|
|
</tr>
|
|||
|
|
</thead>
|
|||
|
|
<tbody>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>visit_occurrence_id</td>
|
|||
|
|
<td align="center">PK</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>person_id</td>
|
|||
|
|
<td align="center">Pid</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>visit_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>visit_source_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>visit_source_value</td>
|
|||
|
|
<td align="center">SV</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">⚠️</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>visit_start_date</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td>Achilles check 1900</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>visit_start_datetime</td>
|
|||
|
|
<td align="center">FC</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>visit_end_date</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>visit_end_datetime</td>
|
|||
|
|
<td align="center">FC</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>visit_type_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>provider_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td>Atlas uses provider.specialty_concept_id</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>care_site_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">⚠️</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td>Achilles only does FK check, Atlas uses
|
|||
|
|
care_site.place_of_service_concept_id</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>admitted_from_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>admitted_from_source_value</td>
|
|||
|
|
<td align="center">SV</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">⚠️</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td>Achilles check 1900</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>discharged_to_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>discharged_to_source_value</td>
|
|||
|
|
<td align="center">SV</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">⚠️</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td>Achilles check 1900</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>VISIT_OCCURRENCE</td>
|
|||
|
|
<td>preceding_visit_occurrence_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
</tbody>
|
|||
|
|
</table>
|
|||
|
|
</div>
|
|||
|
|
<div id="episode" class="section level2">
|
|||
|
|
<h2>Episode</h2>
|
|||
|
|
<table>
|
|||
|
|
<colgroup>
|
|||
|
|
<col width="6%" />
|
|||
|
|
<col width="6%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="11%" />
|
|||
|
|
<col width="6%" />
|
|||
|
|
</colgroup>
|
|||
|
|
<thead>
|
|||
|
|
<tr class="header">
|
|||
|
|
<th>cdmTableName</th>
|
|||
|
|
<th>cdmFieldName</th>
|
|||
|
|
<th align="center">Special Fields</th>
|
|||
|
|
<th align="center">DQD (v1.0)</th>
|
|||
|
|
<th align="center">Achilles (v1.7)</th>
|
|||
|
|
<th align="center">Atlas Cohort (v2.10)</th>
|
|||
|
|
<th align="center">Atlas Cohort (v2.12)</th>
|
|||
|
|
<th align="center">Atlas Data Sources (v2.12)</th>
|
|||
|
|
<th align="center">Feature Extraction (v3.2)</th>
|
|||
|
|
<th>Comment</th>
|
|||
|
|
</tr>
|
|||
|
|
</thead>
|
|||
|
|
<tbody>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_id</td>
|
|||
|
|
<td align="center">PK</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>person_id</td>
|
|||
|
|
<td align="center">Pid</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_start_date</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_start_datetime</td>
|
|||
|
|
<td align="center">FC</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_end_date</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_end_datetime</td>
|
|||
|
|
<td align="center">FC</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_parent_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_number</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_object_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_type_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="even">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_source_value</td>
|
|||
|
|
<td align="center">SV</td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
<tr class="odd">
|
|||
|
|
<td>EPISODE</td>
|
|||
|
|
<td>episode_source_concept_id</td>
|
|||
|
|
<td align="center"></td>
|
|||
|
|
<td align="center">✅</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td align="center">❌</td>
|
|||
|
|
<td></td>
|
|||
|
|
</tr>
|
|||
|
|
</tbody>
|
|||
|
|
</table>
|
|||
|
|
<p>This was an effort by the CDM Working Group in 2022. *Credits: Clair
|
|||
|
|
Blacketer, Maxim Moinat, Nitin Park</p>
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<script>
|
|||
|
|
|
|||
|
|
// add bootstrap table styles to pandoc tables
|
|||
|
|
function bootstrapStylePandocTables() {
|
|||
|
|
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
|
|||
|
|
}
|
|||
|
|
$(document).ready(function () {
|
|||
|
|
bootstrapStylePandocTables();
|
|||
|
|
});
|
|||
|
|
|
|||
|
|
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
<!-- tabsets -->
|
|||
|
|
|
|||
|
|
<script>
|
|||
|
|
$(document).ready(function () {
|
|||
|
|
window.buildTabsets("TOC");
|
|||
|
|
});
|
|||
|
|
|
|||
|
|
$(document).ready(function () {
|
|||
|
|
$('.tabset-dropdown > .nav-tabs > li').click(function () {
|
|||
|
|
$(this).parent().toggleClass('nav-tabs-open');
|
|||
|
|
});
|
|||
|
|
});
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
<!-- code folding -->
|
|||
|
|
|
|||
|
|
<script>
|
|||
|
|
$(document).ready(function () {
|
|||
|
|
|
|||
|
|
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
|
|||
|
|
$('.unlisted.unnumbered').addClass('toc-ignore')
|
|||
|
|
|
|||
|
|
// move toc-ignore selectors from section div to header
|
|||
|
|
$('div.section.toc-ignore')
|
|||
|
|
.removeClass('toc-ignore')
|
|||
|
|
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
|
|||
|
|
|
|||
|
|
// establish options
|
|||
|
|
var options = {
|
|||
|
|
selectors: "h1,h2,h3",
|
|||
|
|
theme: "bootstrap3",
|
|||
|
|
context: '.toc-content',
|
|||
|
|
hashGenerator: function (text) {
|
|||
|
|
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
|
|||
|
|
},
|
|||
|
|
ignoreSelector: ".toc-ignore",
|
|||
|
|
scrollTo: 0
|
|||
|
|
};
|
|||
|
|
options.showAndHide = true;
|
|||
|
|
options.smoothScroll = true;
|
|||
|
|
|
|||
|
|
// tocify
|
|||
|
|
var toc = $("#TOC").tocify(options).data("toc-tocify");
|
|||
|
|
});
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
<!-- dynamically load mathjax for compatibility with self-contained -->
|
|||
|
|
<script>
|
|||
|
|
(function () {
|
|||
|
|
var script = document.createElement("script");
|
|||
|
|
script.type = "text/javascript";
|
|||
|
|
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
|
|||
|
|
document.getElementsByTagName("head")[0].appendChild(script);
|
|||
|
|
})();
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
</body>
|
|||
|
|
</html>
|