Merge remote-tracking branch 'remotes/upstream/main' into snowflake
This commit is contained in:
alex-odysseus
commit
b0685e98c7
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>background.knit</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>CDM v3</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
|
|||
6965
docs/cdm53.html
6965
docs/cdm53.html
File diff suppressed because it is too large
Load Diff
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>OMOP CDM v5.3.1</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
|
|||
7573
docs/cdm54.html
7573
docs/cdm54.html
File diff suppressed because it is too large
Load Diff
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>Changes by Table</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
|
|||
7456
docs/cdm60.html
7456
docs/cdm60.html
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,472 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>cdmDecisionTree.knit</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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 -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<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-home"></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>
|
||||
</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"><div>
|
||||
<img src="ohdsi40x40.png"></img> CDM Request Decision Tree
|
||||
</div></h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>If you have arrived to this page then you must be thinking <strong>HELP! I have some data that doesn’t fit in the CDM!</strong> Never fear as this handy guide will point you in the right direction and all you have to do is answer a few questions.</p>
|
||||
<p><strong>First things first, do you think you will need to change the OMOP Common Data Model itself or are you solely looking for vocabulary support?</strong></p>
|
||||
<p><a href="networkUseCase.html">I think I need to change the OMOP CDM</a></p>
|
||||
<p><a href="vocabN.html">I need vocabulary support</a></p>
|
||||
|
||||
|
||||
|
||||
|
||||
</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 -->
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>Preserving Privacy in an OMOP CDM Implementation</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>CDM R Package Demo</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -60,6 +60,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -85,6 +86,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -236,7 +240,7 @@ $(document).ready(function () {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -252,7 +256,7 @@ $(document).ready(function () {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -272,7 +276,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -292,7 +296,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -310,7 +314,7 @@ $(document).ready(function () {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -323,19 +327,22 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -345,7 +352,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -365,7 +372,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -373,6 +380,9 @@ $(document).ready(function () {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>cdmRefreshProcess.knit</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
@ -485,21 +495,22 @@ div.tocify {
|
|||
|
||||
|
||||
<p>The OMOP Common Data Model is managed by the OHDSI CDM Working Group. The formal remit of the CDM Working Group (WG) is to hear proposals for change, ratifying only those with valid use cases and data to support them. Then, once ratified, these proposals are incorporated into the next version of the CDM. In the past, this was done by the WG alone. The group would invite others from around the community to present use cases for change and suggestions for improvement. The WG would then vote on the proposals and a new CDM version would be released after a certain period of time or if enough proposals were voted in. This approach worked when the community was smaller but as it is growing rapidly the CDM WG needed to adapt the refresh cycle such that everyone has an opportunity to weigh in on the proposed changes.</p>
|
||||
<p>Looking to make a change or addition to the OMOP CDM? Please answer the questions in the <a href="cdmDecisionTree.html">decision tree</a> to point you in the right direction.</p>
|
||||
<div id="cdm-refresh-cycle" class="section level2">
|
||||
<h2>CDM Refresh Cycle</h2>
|
||||
<p><img src="images/CDM_refresh_cycle.png" /></p>
|
||||
<div id="define-new-version-completed-for-v5.4" class="section level3">
|
||||
<h3>1. Define New Version [Completed for v5.4]</h3>
|
||||
<p>The image above describes the new CDM refresh cycle. It begins with <strong>defining a new version</strong>. This has been completed for the current cycle. Issues and proposals on the github were considered during a 4-hour workshop where it was decided the next CDM version will be CDM v5.4, building off of CDM v5.3. The group then participated in a rapid-fire voting activity to identify which changes should be incorporated into CDM v5.4. Any items that were not unanimously agreed upon were then discussed in small groups to hone the proposal and suggestions were presented back to the group. The final roadmap for CDM v5.4 can be found <a href="https://github.com/OHDSI/CommonDataModel/projects/3">here</a>.</p>
|
||||
<p>Looking to open a proposal to change or augment the CDM? Please open an <a href="https://github.com/OHDSI/CommonDataModel/issues">issue</a> and use the <strong>proposal template</strong>.</p>
|
||||
<div id="define-new-version" class="section level3">
|
||||
<h3>1. Define New Version</h3>
|
||||
<p>The image above describes the new CDM refresh cycle. It begins with <strong>defining a new version</strong>. Proposals are heard over the course of a year according to the <a href="cdmRequestProcess.html">CDM Request Process</a> and the ratified changes are added to the roadmap until such time that there are enough updates to warrant a new version of the model.</p>
|
||||
<p>Looking to open a proposal to change or augment the CDM? Please follow the questions in the <a href="cdmDecisionTree.html">decision tree</a> to help you determine what you will need.</p>
|
||||
</div>
|
||||
<div id="sign-off-from-work-groups-completed-for-v5.4" class="section level3">
|
||||
<h3>2. Sign off from Work Groups [Completed for v5.4]</h3>
|
||||
<div id="sign-off-from-work-groups" class="section level3">
|
||||
<h3>2. Sign off from Work Groups</h3>
|
||||
<p>Each member of the CDM WG is a liaison for another workgroup in the community. They are responsible for presenting the proposed changes to the CDM and collecting the feedback. This has resulted in very helpful suggestions from the EHR, Data Quality, Device, HADES, and ACHILLES groups. This outreach has proven to be very effective and should result in a very stable version.</p>
|
||||
</div>
|
||||
<div id="release-ddls" class="section level3">
|
||||
<h3>3. Release DDLs</h3>
|
||||
<p>After all changes and suggestions are agreed upon by the community and work groups the next step is to generate the DDLs. The CDM WG hosted a hackathon on August 18-19, 2021. During this time the group created an R package to automatically generate the DDLs and the code to instantiate an empty CDM instance. Changes were made to v5.3 to generate v5.4 and the repository was refactored.</p>
|
||||
<p>After all changes and suggestions are agreed upon by the community and work groups the next step is to generate the DDLs. For example, the CDM WG hosted a hackathon on August 18-19, 2021. During this time the group created an R package to automatically generate the DDLs and the code to instantiate an empty CDM instance. Changes were made to v5.3 to generate v5.4 and the repository was refactored.</p>
|
||||
</div>
|
||||
<div id="software-update" class="section level3">
|
||||
<h3>4. Software Update</h3>
|
||||
|
|
@ -513,7 +524,7 @@ div.tocify {
|
|||
<div id="cdm-wg-meeting-information" class="section level1">
|
||||
<h1>CDM WG Meeting Information</h1>
|
||||
<p>The CDM working group meets the first and third Tuesday of the month. See below for links to the meetings.</p>
|
||||
<p><strong>Every first Tuesday of the month at 1pm est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d">Teams Meeting</a></p>
|
||||
<p><strong>Every first Tuesday of the month at 10am est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d">Teams Meeting</a></p>
|
||||
<p><strong>Every third Tuesday of the month at 1pm est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1611000164347?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%223c193b7f-c2ab-4bcf-b88c-f89a6b1fba38%22%7d">Teams Meeting</a></p>
|
||||
<p><strong>Note</strong> These were recently changed from a Skype meeting to a Microsoft Teams meeting. If you do you have access to the OHDSI Teams Tenet, please contact Clair Blacketer at <a href="mailto:mblacke@its.jnj.com" class="email">mblacke@its.jnj.com</a>.</p>
|
||||
<div id="cdm-wg-important-links" class="section level3">
|
||||
|
|
|
|||
|
|
@ -0,0 +1,665 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>cdmRequestProcess.knit</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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-home"></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>
|
||||
</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"><div>
|
||||
<img src="ohdsi40x40.png"></img> How to Request Changes to the CDM
|
||||
</div></h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>Are you in the right place? Please answer the questions in the <a href="cdmDecisionTree.html">decision tree</a> prior to beginning a CDM Request to make sure you aren’t missing something.</p>
|
||||
<p>As OHDSI is an open-source community working towards developing a Common Data Model that fulfills the needs of its users, it is often the case that changes need to be made to the model as the community and its research continues to mature. However, the number of people, institutions, and initiatives that rely on the OMOP CDM to advance the science of observational health has grown dramatically since its inception in 2015. Therefore, care must be taken when considering any update to the model, big or small. This document outlines the process that should be taken to ratify a change to the CDM.</p>
|
||||
<p><strong>If you would like guidance prior to starting this process, consider contacting us on our <a href="https://github.com/OHDSI/CommonDataModel">GitHub</a> or <a href="https://teams.microsoft.com/l/team/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/conversations?groupId=a6f2c516-e568-4974-8f1e-a7bdc2f997c5&tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5">Teams Channel</a>.</strong></p>
|
||||
<div id="scope" class="section level3">
|
||||
<h3>Scope</h3>
|
||||
<ul>
|
||||
<li>What kind of changes?
|
||||
<ul>
|
||||
<li>Minor, e.g. new field in existing table</li>
|
||||
<li>Major, e.g. breaking changes, additional tables</li>
|
||||
</ul></li>
|
||||
<li>Who can propose changes?
|
||||
<ul>
|
||||
<li>Individuals, OHDSI working groups, organizations</li>
|
||||
</ul></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="step-1-proposal" class="section level2">
|
||||
<h2>Step 1: Proposal</h2>
|
||||
<p>Once a group or organization has decided on the update they would like made to the model, they must produce a document including the following:</p>
|
||||
<ol style="list-style-type: decimal">
|
||||
<li>A clear description of the change or addition including the User Guide and ETL Conventions in the same structure as what is present on the website for every table and field currently in the CDM.</li>
|
||||
<li>A clearly defined use case noting why the latest version of the OMOP CDM fails to adequately address said use case. This should include describing what you have already tried with the latest version of the OMOP CDM and why it does not meet your needs.</li>
|
||||
<li>An example of how the requested change or addition will be used in practice. This can be in the form of sample data, SQL code, a diagram, or text. The proposal can optionally include suggestions as to how other OHDSI tools (Achilles, DataQualityDashboard, Atlas, etc.) should work with your change or addition.</li>
|
||||
</ol>
|
||||
<p>Once the document is ready to submit, please email <a href="mailto:a58abde7.ohdsi.org@amer.teams.ms">CDM Proposals - Workgroup - Common Data Model</a>. This will go directly to a separate channel in the OHDSI Teams environment that is available to all members of the CDM Working Group. After submitting your document with your proposal to email listed above, someone in the OMOP CDM Working Group will respond to you within 2 weeks. The potential outcomes are as follows:</p>
|
||||
<ul>
|
||||
<li>Proposal merits further review (move on to next steps)</li>
|
||||
<li>Proposal is not ready for workgroup review due to one or more factors
|
||||
<ul>
|
||||
<li>Incomplete</li>
|
||||
<li>Insufficiently aligned with the OMOP framework</li>
|
||||
<li>Poorly described use case</li>
|
||||
</ul></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="step-2-initial-presentation" class="section level2">
|
||||
<h2>Step 2: Initial Presentation</h2>
|
||||
<p>Should your proposals merit further review, the OMOP CDM Working Group will reach out to you to schedule a time for you to present your case at an upcoming meeting. You will be given 15-30 minutes to present your document and you can include anything you feel will help illustrate the need and your potential solution. The group will then discuss, ask questions, and potentially offer other solutions. Depending on the nature of the request, this may go over multiple sessions and you may be asked to make changes to your initial design. At the end of this process your proposal will then be put to consensus in the CDM WG. If the group decides no, they will give feedback describing why they did not feel your proposal should be accepted at this time. If the group decides yes, you move on to step 3.</p>
|
||||
<p><strong>Potential Decision Criteria:</strong></p>
|
||||
<ul>
|
||||
<li>If the change is foundational to OHDSI tools, then the proposal will be put to the larger community open to public comment</li>
|
||||
<li>How generalizable is your change? Can it be readily applied to other use cases?</li>
|
||||
<li>Are the proposed changes/additions well designed from a modeling perspective? Do they follow the existing OMOP CDM conventions?</li>
|
||||
<li>What are the consequences of the change? Are they potentially breaking changes or are they just changes to existing conventions? Will they require the remapping of existing OMOP datasources?</li>
|
||||
<li>How complicated is your change? Is it an addition of a field or multiple tables?</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="step-3-preliminary-decision" class="section level2">
|
||||
<h2>Step 3: Preliminary Decision</h2>
|
||||
<p>If the proposal is accepted in the preliminary decision, then a branch will be created in the CommonDataModel repository, based on the latest version of the OMOP CDM in use (currently v5.4). It will then be your responsibility to apply the change programmatically in this branch. This should include:</p>
|
||||
<ul>
|
||||
<li>Updating the CSV file with the CDM specification, including the User Guide and ETL Conventions documentation</li>
|
||||
<li>Generating the DDL files with the change</li>
|
||||
<li>Testing the new DDL files in at least one supported environment</li>
|
||||
</ul>
|
||||
<p>Once the DDLs with the proposed change are created and tested, you should then ETL some data (either real or synthetic) into the new table/fields. Then, an example cohort should be created that utilizes the change or addition and clearly displays how it can be used in a real study. It is expected that during this stage the proposal will change as you work through your idea in a tangible environment.</p>
|
||||
<p><strong>Potential Decision Criteria:</strong></p>
|
||||
<ul>
|
||||
<li>How would you evaluate the quality of this new field/table?</li>
|
||||
<li>What characterizations would you perform?</li>
|
||||
<li>How would you perform a study using this new feature?</li>
|
||||
</ul>
|
||||
<p><strong>Potential Outcomes:</strong></p>
|
||||
<ul>
|
||||
<li>Proposal demonstrates merit for further consideration as:
|
||||
<ul>
|
||||
<li>a core data model change (move on to next steps)</li>
|
||||
<li>an extension (how do we deal with these/do we have ownership of them?)</li>
|
||||
</ul></li>
|
||||
<li>Proposal does not demonstrate merit for further consideration at this time, and:
|
||||
<ul>
|
||||
<li>recommend as a LOCAL extension</li>
|
||||
<li>recommend a different course</li>
|
||||
</ul></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="step-4-final-presentation" class="section level2">
|
||||
<h2>Step 4: Final Presentation</h2>
|
||||
<p>After generating, testing, and implementing your proposal in a real-world environment the CDM working group will invite you again to present your findings in another 15-30 minute presentation. This should include learnings from the exercise and any updates made to the initial proposal.</p>
|
||||
</div>
|
||||
<div id="step-5-final-decision" class="section level2">
|
||||
<h2>Step 5: Final Decision</h2>
|
||||
<p>At this point, the working group liaisons will also take the proposal to other groups to elicit feedback. Then the CDM working group will vote and give a final decision on the proposed change. If ratified, the branch in the repository will be merged into the develop branch to be included in a next version of the OMOP Common Data Model.</p>
|
||||
<p>The change should initiate requests for features in tools. The end of this process should be a trigger for using the new feature as per the use case. The group should also produce at least one query for the query library on how to work with the new addition/change.</p>
|
||||
<div id="resources" class="section level3">
|
||||
<h3>Resources</h3>
|
||||
<p>“Implementing & adopting a customized OMOP Common Data Model” (Melany Philofsky, OHDSI Symposium 2021) <a href="https://www.ohdsi.org/2021-global-symposium-showcase-18/" class="uri">https://www.ohdsi.org/2021-global-symposium-showcase-18/</a></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>
|
||||
|
|
@ -0,0 +1,469 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>Contact the Vocab Team</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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 -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<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-home"></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>
|
||||
</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">Contact the Vocab Team</h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>Okay so you have something you would like to add to the CDM but there is not an existing OMOP vocabulary nor an open-source vocabulary we can bring in to support it. <strong>In this case, please contact the vocabulary team on next steps</strong> as data elements in the CDM must have a vocabulary in place before they can be implemented.</p>
|
||||
<p><a href="https://teams.microsoft.com/l/channel/19%3a31208179438d45749ff484124e7b1e5e%40thread.tacv2/Vocabulary%2520Subgroup?groupId=a6f2c516-e568-4974-8f1e-a7bdc2f997c5&tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5">Vocabulary Teams Channel</a></p>
|
||||
<p>Once you come to consensus with the vocabulary team regarding your needs, please follow the <a href="cdmRequestProcess.html">CDM Request Process</a> to begin the steps soliciting a change or addition to the model itself. Need more guidance? Consider contacting the CDM Working Group on our <a href="https://github.com/OHDSI/CommonDataModel">GitHub</a> or <a href="https://teams.microsoft.com/l/team/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/conversations?groupId=a6f2c516-e568-4974-8f1e-a7bdc2f997c5&tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5">Teams Channel</a>.</p>
|
||||
|
||||
|
||||
|
||||
|
||||
</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 -->
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>Ask A Question</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>dataModelConventions.knit</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>Download</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@
|
|||
|
||||
<title>drug_dose.knit</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -62,6 +62,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -87,6 +88,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -238,7 +242,7 @@ $(document).ready(function () {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -254,7 +258,7 @@ $(document).ready(function () {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -274,7 +278,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -294,7 +298,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -312,7 +316,7 @@ $(document).ready(function () {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -325,19 +329,22 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -347,7 +354,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -367,7 +374,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -375,6 +382,9 @@ $(document).ready(function () {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>Observation Period Considerations for EHR Data</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -60,6 +60,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -85,6 +86,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -236,7 +240,7 @@ $(document).ready(function () {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -252,7 +256,7 @@ $(document).ready(function () {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -272,7 +276,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -292,7 +296,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -310,7 +314,7 @@ $(document).ready(function () {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -323,19 +327,22 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -345,7 +352,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -365,7 +372,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -373,6 +380,9 @@ $(document).ready(function () {
|
|||
<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>
|
||||
|
|
|
|||
164
docs/faq.html
164
docs/faq.html
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>OMOP CDM Frequently Asked Questions</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -29,6 +29,9 @@
|
|||
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>
|
||||
|
|
@ -60,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -85,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -222,6 +229,69 @@ $(document).ready(function () {
|
|||
|
||||
|
||||
|
||||
<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>
|
||||
|
||||
|
|
@ -231,12 +301,22 @@ $(document).ready(function () {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -252,7 +332,7 @@ $(document).ready(function () {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -272,7 +352,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -292,7 +372,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -310,7 +390,7 @@ $(document).ready(function () {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -323,19 +403,22 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -345,7 +428,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -365,7 +448,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -373,6 +456,9 @@ $(document).ready(function () {
|
|||
<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>
|
||||
|
|
@ -504,9 +590,36 @@ $(document).ready(function () {
|
|||
<p>OHDSI runs as a distributed data network. All analyses are publicly available and can be downloaded to run at each site. The packages can be run locally and, at the data partner’s discretion, aggregate results can be shared with the study coordinator.</p>
|
||||
<p>Data partners can also make use of one of OHDSI’s open-source tools called <a href="https://github.com/OHDSI/arachne">ARACHNE</a>, a tool to facilitate distributed network analytics against the OMOP CDM.</p>
|
||||
</div>
|
||||
<div id="recommended-system-requirements" class="section level2">
|
||||
<h2>Recommended System Requirements</h2>
|
||||
<p>It is difficult to recommend what technical capabilities a site needs to set up an ETL because it is heavily dependent on the amount of data they have and how they plan to use it. Here are some examples of options that have worked well for small to medium organizations and large organizations:</p>
|
||||
<p><strong>Small-to-Medium Organization</strong></p>
|
||||
<ul>
|
||||
<li>CDM size is 100MB to several GBs</li>
|
||||
<li>Vocab ~20GB</li>
|
||||
<li>Results < 500 MB</li>
|
||||
<li>Recommend
|
||||
<ul>
|
||||
<li>Server class machine disk >= 250GB (SSD preferred), >= 4 cores, >= 32GB RAM</li>
|
||||
</ul></li>
|
||||
</ul>
|
||||
<p><strong>Large Organization</strong></p>
|
||||
<ul>
|
||||
<li>CDM size is 12GB to several TBs</li>
|
||||
<li>Vocab ~20GB</li>
|
||||
<li>Results < 500 MB</li>
|
||||
<li>Recommend
|
||||
<ul>
|
||||
<li>Cloud-based infrastructure like multiple AWS Redshift clusters, for example:</li>
|
||||
<li><img src="images/AWS_clusters.png" /></li>
|
||||
</ul></li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
|
||||
|
|
@ -539,6 +652,35 @@ $(document).ready(function () {
|
|||
|
||||
<!-- 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,h4,h5",
|
||||
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>
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 38 KiB |
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>index.knit</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -60,6 +60,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -85,6 +86,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -236,7 +240,7 @@ $(document).ready(function () {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -252,7 +256,7 @@ $(document).ready(function () {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -272,7 +276,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -292,7 +296,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -310,7 +314,7 @@ $(document).ready(function () {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -323,19 +327,22 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -345,7 +352,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -365,7 +372,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -373,6 +380,9 @@ $(document).ready(function () {
|
|||
<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>
|
||||
|
|
@ -497,9 +507,9 @@ $(document).ready(function () {
|
|||
<div id="meeting-information" class="section level3">
|
||||
<h3>Meeting Information</h3>
|
||||
<p>The CDM working group meets the first and third Tuesday of the month. See below for links to the meetings.</p>
|
||||
<p><strong>Every first Tuesday of the month at 1pm est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d">Teams Meeting</a></p>
|
||||
<p><strong>Every first Tuesday of the month at 10am est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d">Teams Meeting</a></p>
|
||||
<p><strong>Every third Tuesday of the month at 1pm est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1611000164347?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%223c193b7f-c2ab-4bcf-b88c-f89a6b1fba38%22%7d">Teams Meeting</a></p>
|
||||
<p><strong>Note</strong> If you do you have access to the OHDSI Teams Tenet, either contact Clair Blacketer at <a href="mailto:mblacke@its.jnj.com" class="email">mblacke@its.jnj.com</a> or fill out [this form] (<a href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu" class="uri">https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu</a>) and check “Common Data Model”</p>
|
||||
<p><strong>Note</strong> If you do you have access to the OHDSI Teams Tenet, either contact Clair Blacketer at <a href="mailto:mblacke@its.jnj.com" class="email">mblacke@its.jnj.com</a> or fill out <a href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu">this form</a> and check “Common Data Model”</p>
|
||||
</div>
|
||||
<div id="cdm-wg-important-links" class="section level3">
|
||||
<h3>CDM WG Important Links</h3>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>Indices, Primary Keys and Foreign Key Constraints</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,467 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>Leave As Is</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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 -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<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-home"></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>
|
||||
</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">Leave As Is</h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>Okay, so you do not have a network use case but multiple collaborators have access to the element you are interested in adding to the CDM. <strong>In this circumstance, the CDM Working Group suggests leaving the model as-is.</strong> Without a network use case there is no need to augment the data model. If this is something you need for your work, consider a <a href="localChange.html">local change</a> or a model extension.</p>
|
||||
|
||||
|
||||
|
||||
|
||||
</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 -->
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
@ -0,0 +1,467 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>Local Change</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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 -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<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-home"></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>
|
||||
</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">Local Change</h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>Since you do not have a network use case and this element is specific to your data source, <strong>feel free to create a local change to your instance of the OMOP Common Data Model.</strong> Augmenting the model at your institution for administrative purposes or other in-house needs is totally acceptable with the understanding that any local changes cannot and should not be relied upon in network studies or supported by the open-source tools.</p>
|
||||
|
||||
|
||||
|
||||
|
||||
</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 -->
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
@ -0,0 +1,469 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>Network Use Case</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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 -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<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-home"></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>
|
||||
</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">Network Use Case</h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>Alright, so you think you might need to change the OMOP Common Data Model. <strong>Do you have a documented network use case for this data need? This could take the form of an upcoming study or a convention for how to store information.</strong> In this scenario, at least two or more collaborators with data to contribute constitute a network need.</p>
|
||||
<p><a href="useCaseY.html">Yes, I have a network use case</a></p>
|
||||
<p><a href="useCaseN.html">No, I do not have a network use case</a></p>
|
||||
|
||||
|
||||
|
||||
|
||||
</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 -->
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>Oncology Extension</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
@ -486,429 +496,14 @@ div.tocify {
|
|||
<h2>OMOP Common Data Model Oncology Extension Documentation</h2>
|
||||
<p>This documentation details the ratified proposal of adding an oncology extension to the OMOP CDM. These tables and fields will become part of the next release (v6.1) of the Common Data Model. Below are their descriptions; showing <em>additions</em> to the model only. For example, two fields were added to the MEASUREMENT table as part of this extension so only those two fields are listed below for MEASUREMENT instead of the entire table. For more information, please see the <a href="https://github.com/OHDSI/OncologyWG/wiki">OMOP Oncology wiki site</a>.</p>
|
||||
<p>The DDLs for these tables are located on the Oncology github, as detailed in the <a href="https://github.com/OHDSI/OncologyWG/wiki/Oncology-CDM-Extension-Installation">installation instructions</a>.</p>
|
||||
<pre><code>## Warning in read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on '../inst/csv/
|
||||
## OMOP_CDM_Oncology_Ex_Table_Level.csv'</code></pre>
|
||||
<pre><code>## Warning in read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found
|
||||
## by readTableHeader on '../inst/csv/OMOP_CDM_Oncology_Ex_Table_Level.csv'</code></pre>
|
||||
<div id="episode" class="section level3 tabset tabset-pills">
|
||||
<h3 class="tabset tabset-pills">EPISODE</h3>
|
||||
<p><strong>Table Description</strong></p>
|
||||
<p>The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) into a higher-level abstraction representing clinically and analytically relevant disease phases,outcomes and treatments. The EPISODE_EVENT table connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry. For example cancers including their development over time, their treatment, and final resolution.</p>
|
||||
<p><strong>User Guide</strong></p>
|
||||
<p>Valid Episode Concepts belong to the ‘Episode’ domain. For cancer episodes please see [article], for non-cancer episodes please see [article]. If your source data does not have all episodes that are relevant to the therapeutic area, write only those you can easily derive from the data. It is understood that that table is not currently expected to be comprehensive.</p>
|
||||
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
|
||||
<thead>
|
||||
<tr>
|
||||
<th style="text-align:left;">
|
||||
CDM Field
|
||||
</th>
|
||||
<th style="text-align:left;width: 3in; ">
|
||||
User Guide
|
||||
</th>
|
||||
<th style="text-align:left;width: 4in; ">
|
||||
ETL Conventions
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Datatype
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Required
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Primary Key
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Foreign Key
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Table
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Domain
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Class
|
||||
</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A unique identifier for each Episode.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
person_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The PERSON_ID of the PERSON for whom the episode is recorded.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
PERSON
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see [article] for cancers and [article] for non-cancers describing how these are defined. <a href="https://athena.ohdsi.org/search-terms/terms?domain=Episode&page=1&pageSize=15&query=">Accepted Concepts</a>
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Episode
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_start_date
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The date when the Episode beings.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Please see [article] for how to define an Episode start date.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
date
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_start_datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The date and time when the Episode begins.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_end_date
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The date when the instance of the Episode is considered to have ended.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Please see [article] for how to define an Episode end date.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
date
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_end_datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The date when the instance of the Episode is considered to have ended.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_parent_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
Use this field to find the Episode that subsumes the given Episode record. This is used in the case that an Episode are nested into each other.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
If there are multiple nested levels to how Episodes are represented, the EPISODE_PARENT_ID can be used to record this relationship.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_number
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
For sequences of episodes, this is used to indicate the order the episodes occurred. For example, lines of treatment could be indicated here.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Please see [article] for the details of how to count episodes.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_object_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A Standard Concept representing the disease phase, outcome, or other abstraction of which the episode consists. For example, if the EPISODE_CONCEPT_ID is <a href="https://athena.ohdsi.org/search-terms/terms/32531">treatment regimen</a> then the EPISODE_OBJECT_CONCEPT_ID should contain the chemotherapy regimen concept, like <a href="https://athena.ohdsi.org/search-terms/terms/35804392">Afatinib monotherapy</a>.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Episode entries from the ‘Disease Episode’ concept class should have an episode_object_concept_id that comes from the Condition domain. Episode entries from the ‘Treatment Episode’ concept class should have an episode_object_concept_id that scome from the ‘Procedure’ domain or ‘Regimen’ concept class.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Procedure, Regimen
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_type_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
This field can be used to determine the provenance of the Episode record, as in whether the episode was from an EHR system, insurance claim, registry, or other sources.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Choose the EPISODE_TYPE_CONCEPT_ID that best represents the provenance of the record. <a href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=">Accepted Concepts</a>.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Type Concept
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_source_value
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The source code for the Episdoe as it appears in the source data. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
varchar(50)
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_source_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key to a Episode Concept that refers to the code used in the source.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Given that the Episodes are user-defined it is unlikely that there will be a Source Concept available. If that is the case then set this field to zero.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div id="episode_event" class="section level3 tabset tabset-pills">
|
||||
<h3 class="tabset tabset-pills">EPISODE_EVENT</h3>
|
||||
|
|
@ -918,134 +513,6 @@ CONCEPT
|
|||
<p>This connecting table is used instead of the FACT_RELATIONSHIP table for linking low-level events to abstracted Episodes.</p>
|
||||
<p><strong>ETL Conventions</strong></p>
|
||||
<p>Some episodes may not have links to any underlying clinical events. For such episodes, the EPISODE_EVENT table is not populated.</p>
|
||||
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
|
||||
<thead>
|
||||
<tr>
|
||||
<th style="text-align:left;">
|
||||
CDM Field
|
||||
</th>
|
||||
<th style="text-align:left;width: 3in; ">
|
||||
User Guide
|
||||
</th>
|
||||
<th style="text-align:left;width: 4in; ">
|
||||
ETL Conventions
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Datatype
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Required
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Primary Key
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Foreign Key
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Table
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Domain
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Class
|
||||
</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
Use this field to link the EPISODE_EVENT record to its EPISODE.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the EPISODE_ID that subsumes the EPISODE_EVENT record here.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
EPISODE
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
event_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
This field is the primary key of the linked record in the database. For example, if the Episode Event is a Condition Occurrence, then the CONDITION_OCCURRENCE_ID of the linked record goes in this field.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the primary key of the linked record here.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_event_field_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
This field is the CONCEPT_ID that identifies which table the primary key of the linked record came from.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the CONCEPT_ID that identifies which table and field the EVENT_ID came from. <a href="https://athena.ohdsi.org/search-terms/terms?vocabulary=CDM&conceptClass=Field&page=1&pageSize=15&query=">Accepted Concepts</a>
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Metadata
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div id="measurement" class="section level3 tabset tabset-pills">
|
||||
<h3 class="tabset tabset-pills">MEASUREMENT</h3>
|
||||
|
|
@ -1053,104 +520,6 @@ Metadata
|
|||
<p>The MEASUREMENT table contains records of Measurement, i.e. structured values (numerical or categorical) obtained through systematic and standardized examination or testing of a Person or Person’s sample. The MEASUREMENT table contains both orders and results of such Measurements as laboratory tests, vital signs, quantitative findings from pathology reports, etc. Measurements are stored as attribute value pairs, with the attribute as the Measurement Concept and the value representing the result. The value can be a Concept (stored in VALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with a Unit (UNIT_CONCEPT_ID).</p>
|
||||
<p><strong>User Guide</strong></p>
|
||||
<p>Measurements differ from Observations in that they require a standardized test or some other activity to generate a quantitative or qualitative result.</p>
|
||||
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
|
||||
<thead>
|
||||
<tr>
|
||||
<th style="text-align:left;">
|
||||
CDM Field
|
||||
</th>
|
||||
<th style="text-align:left;width: 3in; ">
|
||||
User Guide
|
||||
</th>
|
||||
<th style="text-align:left;width: 4in; ">
|
||||
ETL Conventions
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Datatype
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Required
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Primary Key
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Foreign Key
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Table
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Domain
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Class
|
||||
</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
modifier_of_event_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
If the Measurement record is related to another record in the database, this field is the primary key of the linked record.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the primary key of the linked record, if applicable, here.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
modifier_of_field_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
If the Measurement record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the CONCEPT_ID that identifies which table and field the MODIFIER_OF_EVENT_ID came from. <a href="https://athena.ohdsi.org/search-terms/terms?vocabulary=CDM&conceptClass=Field&page=1&pageSize=15&query=">Accepted Concepts</a>
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Metadata
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@
|
|||
|
||||
<title>Example_Queries</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -62,6 +62,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -87,6 +88,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -238,7 +242,7 @@ $(document).ready(function () {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -254,7 +258,7 @@ $(document).ready(function () {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -274,7 +278,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -294,7 +298,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -312,7 +316,7 @@ $(document).ready(function () {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -325,19 +329,22 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -347,7 +354,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -367,7 +374,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -375,6 +382,9 @@ $(document).ready(function () {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>CDM Proposals Under Review</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -60,6 +60,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -85,6 +86,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -236,7 +240,7 @@ $(document).ready(function () {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -252,7 +256,7 @@ $(document).ready(function () {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -272,7 +276,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -292,7 +296,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -310,7 +314,7 @@ $(document).ready(function () {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -323,19 +327,22 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -345,7 +352,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -365,7 +372,7 @@ $(document).ready(function () {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -373,6 +380,9 @@ $(document).ready(function () {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -34,7 +34,9 @@ window.initializeCodeFolding = function(show) {
|
|||
showCodeButton.append(showCodeText);
|
||||
showCodeButton
|
||||
.attr('data-toggle', 'collapse')
|
||||
.attr('data-bs-toggle', 'collapse') // BS5
|
||||
.attr('data-target', '#' + id)
|
||||
.attr('data-bs-target', '#' + id) // BS5
|
||||
.attr('aria-expanded', showThis)
|
||||
.attr('aria-controls', id);
|
||||
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>sqlScripts.knit</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
@ -698,176 +708,170 @@ GROUP BY person_id
|
|||
</div>
|
||||
<div id="drug-eras" class="section level3">
|
||||
<h3>Drug Eras</h3>
|
||||
<p>If the DRUG_EXPOSURE table is populated this script will string together periods of time that a person is exposed to an active drug ingredient, allowing for 30 gaps in between. It will then insert the resulting era records into the DRUG_ERA table. <strong>NOTE</strong> This query only works with 5.3 and below.</p>
|
||||
<p>If the DRUG_EXPOSURE table is populated this script will string together periods of time that a person is exposed to an active drug ingredient, allowing for 30 gaps in between. It will then insert the resulting era records into the DRUG_ERA table. <strong>NOTE</strong> This query only works with the <strong>version 5</strong> series and below.</p>
|
||||
<pre class="sql"><code>
|
||||
/****************************************************
|
||||
OHDSI-SQL File Instructions
|
||||
-----------------------------
|
||||
1. Set parameter name of schema that contains CDMv4 instance
|
||||
(@SOURCE_CDMV4, @SOURCE_CDMV4_SCHEMA)
|
||||
2. Set parameter name of schema that contains CDMv5 instance
|
||||
(@TARGET_CDMV5, @TARGET_CDMV5_SCHEMA)
|
||||
3. Run this script through SqlRender to produce a script that will work in your
|
||||
source dialect. SqlRender can be found here: https://github.com/OHDSI/SqlRender
|
||||
4. Run the script produced by SQL Render on your target RDBDMS.
|
||||
<RDBMS> File Instructions
|
||||
-------------------------
|
||||
1. This script will hold a number of placeholders for your CDM V4 and CDMV5
|
||||
database/schema. In order to make this file work in your environment, you
|
||||
should plan to do a global "FIND AND REPLACE" on this file to fill in the
|
||||
file with values that pertain to your environment. The following are the
|
||||
tokens you should use when doing your "FIND AND REPLACE" operation:
|
||||
|
||||
[CDM]
|
||||
[CDM].[CDMSCHEMA]
|
||||
|
||||
*********************************************************************************/
|
||||
/* SCRIPT PARAMETERS */
|
||||
|
||||
|
||||
{DEFAULT @TARGET_CDMV5 = '[CDM]' } -- The target CDMv5 database name
|
||||
{DEFAULT @TARGET_CDMV5_SCHEMA = '[CDM].[CDMSCHEMA]' } -- the target CDMv5 database plus schema
|
||||
|
||||
USE @TARGET_CDMV5;
|
||||
-- Code taken from:
|
||||
-- https://github.com/OHDSI/ETL-CMS/blob/master/SQL/create_CDMv5_drug_era_non_stockpile.sql
|
||||
|
||||
|
||||
if object_id('tempdb..#tmp_de', 'U') is not null drop table #tmp_de;
|
||||
|
||||
/****
|
||||
DRUG ERA
|
||||
Note: Eras derived from DRUG_EXPOSURE table, using 30d gap
|
||||
****/
|
||||
IF OBJECT_ID('tempdb..#cteDrugTarget', 'U') IS NOT NULL
|
||||
DROP TABLE #cteDrugTarget;
|
||||
WITH
|
||||
ctePreDrugTarget(drug_exposure_id, person_id, ingredient_concept_id, drug_exposure_start_date, days_supply, drug_exposure_end_date) AS
|
||||
(-- Normalize DRUG_EXPOSURE_END_DATE to either the existing drug exposure end date, or add days supply, or add 1 day to the start date
|
||||
SELECT
|
||||
d.drug_exposure_id
|
||||
, d.person_id
|
||||
, c.concept_id AS ingredient_concept_id
|
||||
, d.drug_exposure_start_date AS drug_exposure_start_date
|
||||
, d.days_supply AS days_supply
|
||||
, COALESCE(
|
||||
---NULLIF returns NULL if both values are the same, otherwise it returns the first parameter
|
||||
NULLIF(drug_exposure_end_date, NULL),
|
||||
---If drug_exposure_end_date != NULL, return drug_exposure_end_date, otherwise go to next case
|
||||
NULLIF(dateadd(day,days_supply,drug_exposure_start_date), drug_exposure_start_date),
|
||||
---If days_supply != NULL or 0, return drug_exposure_start_date + days_supply, otherwise go to next case
|
||||
dateadd(day,1,drug_exposure_start_date)
|
||||
---Add 1 day to the drug_exposure_start_date since there is no end_date or INTERVAL for the days_supply
|
||||
) AS drug_exposure_end_date
|
||||
FROM @cdm_schema.drug_exposure d
|
||||
JOIN @cdm_schema.concept_ancestor ca ON ca.descendant_concept_id = d.drug_concept_id
|
||||
JOIN @cdm_schema.concept c ON ca.ancestor_concept_id = c.concept_id
|
||||
WHERE c.vocabulary_id = 'RxNorm' ---8 selects RxNorm from the vocabulary_id
|
||||
AND c.concept_class_id = 'Ingredient'
|
||||
AND d.drug_concept_id != 0 ---Our unmapped drug_concept_id's are set to 0, so we don't want different drugs wrapped up in the same era
|
||||
AND coalesce(d.days_supply,0) >= 0 ---We have cases where days_supply is negative, and this can set the end_date before the start_date, which we don't want. So we're just looking over those rows. This is a data-quality issue.
|
||||
)
|
||||
|
||||
/* / */
|
||||
|
||||
-- Normalize DRUG_EXPOSURE_END_DATE to either the existing drug exposure end date, or add days supply, or add 1 day to the start date
|
||||
SELECT d.DRUG_EXPOSURE_ID
|
||||
,d.PERSON_ID
|
||||
,c.CONCEPT_ID
|
||||
,d.DRUG_TYPE_CONCEPT_ID
|
||||
,DRUG_EXPOSURE_START_DATE
|
||||
,COALESCE(DRUG_EXPOSURE_END_DATE, DATEADD(day, DAYS_SUPPLY, DRUG_EXPOSURE_START_DATE), DATEADD(day, 1, DRUG_EXPOSURE_START_DATE)) AS DRUG_EXPOSURE_END_DATE
|
||||
,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
|
||||
INTO #cteDrugTarget
|
||||
FROM @TARGET_CDMV5_SCHEMA.DRUG_EXPOSURE d
|
||||
INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
|
||||
INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
|
||||
WHERE c.DOMAIN_ID = 'Drug'
|
||||
AND c.CONCEPT_CLASS_ID = 'Ingredient'
|
||||
AND c.STANDARD_CONCEPT = 'S';
|
||||
|
||||
/* / */
|
||||
|
||||
IF OBJECT_ID('tempdb..#cteEndDates', 'U') IS NOT NULL
|
||||
DROP TABLE #cteEndDates;
|
||||
|
||||
/* / */
|
||||
|
||||
SELECT PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,DATEADD(day, - 30, EVENT_DATE) AS END_DATE -- unpad the end date
|
||||
INTO #cteEndDates
|
||||
FROM (
|
||||
SELECT E1.PERSON_ID
|
||||
,E1.INGREDIENT_CONCEPT_ID
|
||||
,E1.EVENT_DATE
|
||||
,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL
|
||||
,E1.OVERALL_ORD
|
||||
FROM (
|
||||
SELECT PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,EVENT_DATE
|
||||
,EVENT_TYPE
|
||||
,START_ORDINAL
|
||||
,ROW_NUMBER() OVER (
|
||||
PARTITION BY PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID ORDER BY EVENT_DATE
|
||||
,EVENT_TYPE
|
||||
) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date
|
||||
, cteSubExposureEndDates (person_id, ingredient_concept_id, end_date) AS --- A preliminary sorting that groups all of the overlapping exposures into one exposure so that we don't double-count non-gap-days
|
||||
(
|
||||
SELECT person_id, ingredient_concept_id, event_date AS end_date
|
||||
FROM
|
||||
(
|
||||
SELECT person_id, ingredient_concept_id, event_date, event_type,
|
||||
MAX(start_ordinal) OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY event_date, event_type ROWS unbounded preceding) AS start_ordinal,
|
||||
-- this pulls the current START down from the prior rows so that the NULLs
|
||||
-- from the END DATES will contain a value we can compare with
|
||||
ROW_NUMBER() OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY event_date, event_type) AS overall_ord
|
||||
-- this re-numbers the inner UNION so all rows are numbered ordered by the event date
|
||||
FROM (
|
||||
-- select the start dates, assigning a row number to each
|
||||
SELECT PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,DRUG_EXPOSURE_START_DATE AS EVENT_DATE
|
||||
,0 AS EVENT_TYPE
|
||||
,ROW_NUMBER() OVER (
|
||||
PARTITION BY PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM #cteDrugTarget
|
||||
SELECT person_id, ingredient_concept_id, drug_exposure_start_date AS event_date,
|
||||
-1 AS event_type,
|
||||
ROW_NUMBER() OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY drug_exposure_start_date) AS start_ordinal
|
||||
FROM ctePreDrugTarget
|
||||
|
||||
UNION ALL
|
||||
|
||||
-- add the end dates with NULL as the row number, padding the end dates by 30 to allow a grace period for overlapping ranges.
|
||||
SELECT PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,DATEADD(day, 30, DRUG_EXPOSURE_END_DATE)
|
||||
,1 AS EVENT_TYPE
|
||||
,NULL
|
||||
FROM #cteDrugTarget
|
||||
) RAWDATA
|
||||
) E1
|
||||
INNER JOIN (
|
||||
SELECT PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,DRUG_EXPOSURE_START_DATE AS EVENT_DATE
|
||||
,ROW_NUMBER() OVER (
|
||||
PARTITION BY PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM #cteDrugTarget
|
||||
) E2 ON E1.PERSON_ID = E2.PERSON_ID
|
||||
AND E1.INGREDIENT_CONCEPT_ID = E2.INGREDIENT_CONCEPT_ID
|
||||
AND E2.EVENT_DATE <= E1.EVENT_DATE
|
||||
GROUP BY E1.PERSON_ID
|
||||
,E1.INGREDIENT_CONCEPT_ID
|
||||
,E1.EVENT_DATE
|
||||
,E1.START_ORDINAL
|
||||
,E1.OVERALL_ORD
|
||||
) E
|
||||
WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0;
|
||||
SELECT person_id, ingredient_concept_id, drug_exposure_end_date, 1 AS event_type, NULL
|
||||
FROM ctePreDrugTarget
|
||||
) RAWDATA
|
||||
) e
|
||||
WHERE (2 * e.start_ordinal) - e.overall_ord = 0
|
||||
)
|
||||
|
||||
/* / */
|
||||
, cteDrugExposureEnds (person_id, drug_concept_id, drug_exposure_start_date, drug_sub_exposure_end_date) AS
|
||||
(
|
||||
SELECT
|
||||
dt.person_id
|
||||
, dt.ingredient_concept_id
|
||||
, dt.drug_exposure_start_date
|
||||
, MIN(e.end_date) AS drug_sub_exposure_end_date
|
||||
FROM ctePreDrugTarget dt
|
||||
JOIN cteSubExposureEndDates e ON dt.person_id = e.person_id AND dt.ingredient_concept_id = e.ingredient_concept_id AND e.end_date >= dt.drug_exposure_start_date
|
||||
GROUP BY
|
||||
dt.drug_exposure_id
|
||||
, dt.person_id
|
||||
, dt.ingredient_concept_id
|
||||
, dt.drug_exposure_start_date
|
||||
)
|
||||
--------------------------------------------------------------------------------------------------------------
|
||||
, cteSubExposures(row_number, person_id, drug_concept_id, drug_sub_exposure_start_date, drug_sub_exposure_end_date, drug_exposure_count) AS
|
||||
(
|
||||
SELECT ROW_NUMBER() OVER (PARTITION BY person_id, drug_concept_id, drug_sub_exposure_end_date ORDER BY person_id)
|
||||
, person_id, drug_concept_id, MIN(drug_exposure_start_date) AS drug_sub_exposure_start_date, drug_sub_exposure_end_date, COUNT(*) AS drug_exposure_count
|
||||
FROM cteDrugExposureEnds
|
||||
GROUP BY person_id, drug_concept_id, drug_sub_exposure_end_date
|
||||
--ORDER BY person_id, drug_concept_id
|
||||
)
|
||||
--------------------------------------------------------------------------------------------------------------
|
||||
/*Everything above grouped exposures into sub_exposures if there was overlap between exposures.
|
||||
*So there was no persistence window. Now we can add the persistence window to calculate eras.
|
||||
*/
|
||||
--------------------------------------------------------------------------------------------------------------
|
||||
, cteFinalTarget(row_number, person_id, ingredient_concept_id, drug_sub_exposure_start_date, drug_sub_exposure_end_date, drug_exposure_count, days_exposed) AS
|
||||
(
|
||||
SELECT row_number, person_id, drug_concept_id, drug_sub_exposure_start_date, drug_sub_exposure_end_date, drug_exposure_count
|
||||
, datediff(day,drug_sub_exposure_start_date,drug_sub_exposure_end_date) AS days_exposed
|
||||
FROM cteSubExposures
|
||||
)
|
||||
--------------------------------------------------------------------------------------------------------------
|
||||
, cteEndDates (person_id, ingredient_concept_id, end_date) AS -- the magic
|
||||
(
|
||||
SELECT person_id, ingredient_concept_id, dateadd(day,-30,event_date) AS end_date -- unpad the end date
|
||||
FROM
|
||||
(
|
||||
SELECT person_id, ingredient_concept_id, event_date, event_type,
|
||||
MAX(start_ordinal) OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY event_date, event_type ROWS UNBOUNDED PRECEDING) AS start_ordinal,
|
||||
-- this pulls the current START down from the prior rows so that the NULLs
|
||||
-- from the END DATES will contain a value we can compare with
|
||||
ROW_NUMBER() OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY event_date, event_type) AS overall_ord
|
||||
-- this re-numbers the inner UNION so all rows are numbered ordered by the event date
|
||||
FROM (
|
||||
-- select the start dates, assigning a row number to each
|
||||
SELECT person_id, ingredient_concept_id, drug_sub_exposure_start_date AS event_date,
|
||||
-1 AS event_type,
|
||||
ROW_NUMBER() OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY drug_sub_exposure_start_date) AS start_ordinal
|
||||
FROM cteFinalTarget
|
||||
|
||||
IF OBJECT_ID('tempdb..#cteDrugExpEnds', 'U') IS NOT NULL
|
||||
DROP TABLE #cteDrugExpEnds;
|
||||
UNION ALL
|
||||
|
||||
/* / */
|
||||
-- pad the end dates by 30 to allow a grace period for overlapping ranges.
|
||||
SELECT person_id, ingredient_concept_id, dateadd(day,30,drug_sub_exposure_end_date), 1 AS event_type, NULL
|
||||
FROM cteFinalTarget
|
||||
) RAWDATA
|
||||
) e
|
||||
WHERE (2 * e.start_ordinal) - e.overall_ord = 0
|
||||
|
||||
SELECT d.PERSON_ID
|
||||
,d.INGREDIENT_CONCEPT_ID
|
||||
,d.DRUG_TYPE_CONCEPT_ID
|
||||
,d.DRUG_EXPOSURE_START_DATE
|
||||
,MIN(e.END_DATE) AS ERA_END_DATE
|
||||
INTO #cteDrugExpEnds
|
||||
FROM #cteDrugTarget d
|
||||
INNER JOIN #cteEndDates e ON d.PERSON_ID = e.PERSON_ID
|
||||
AND d.INGREDIENT_CONCEPT_ID = e.INGREDIENT_CONCEPT_ID
|
||||
AND e.END_DATE >= d.DRUG_EXPOSURE_START_DATE
|
||||
GROUP BY d.PERSON_ID
|
||||
,d.INGREDIENT_CONCEPT_ID
|
||||
,d.DRUG_TYPE_CONCEPT_ID
|
||||
,d.DRUG_EXPOSURE_START_DATE;
|
||||
)
|
||||
, cteDrugEraEnds (person_id, drug_concept_id, drug_sub_exposure_start_date, drug_era_end_date, drug_exposure_count, days_exposed) AS
|
||||
(
|
||||
SELECT
|
||||
ft.person_id
|
||||
, ft.ingredient_concept_id
|
||||
, ft.drug_sub_exposure_start_date
|
||||
, MIN(e.end_date) AS era_end_date
|
||||
, drug_exposure_count
|
||||
, days_exposed
|
||||
FROM cteFinalTarget ft
|
||||
JOIN cteEndDates e ON ft.person_id = e.person_id AND ft.ingredient_concept_id = e.ingredient_concept_id AND e.end_date >= ft.drug_sub_exposure_start_date
|
||||
GROUP BY
|
||||
ft.person_id
|
||||
, ft.ingredient_concept_id
|
||||
, ft.drug_sub_exposure_start_date
|
||||
, drug_exposure_count
|
||||
, days_exposed
|
||||
)
|
||||
SELECT
|
||||
row_number()over(order by person_id) drug_era_id
|
||||
, person_id
|
||||
, drug_concept_id
|
||||
, MIN(drug_sub_exposure_start_date) AS drug_era_start_date
|
||||
, drug_era_end_date
|
||||
, SUM(drug_exposure_count) AS drug_exposure_count
|
||||
, datediff(day,MIN(drug_sub_exposure_start_date),drug_era_end_date)-SUM(days_exposed) as gap_days
|
||||
INTO #tmp_de
|
||||
FROM cteDrugEraEnds dee
|
||||
GROUP BY person_id, drug_concept_id, drug_era_end_date;
|
||||
|
||||
/* / */
|
||||
|
||||
INSERT INTO @TARGET_CDMV5_SCHEMA.drug_era
|
||||
SELECT row_number() OVER (
|
||||
ORDER BY person_id
|
||||
) AS drug_era_id
|
||||
,person_id
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,min(DRUG_EXPOSURE_START_DATE) AS drug_era_start_date
|
||||
,ERA_END_DATE
|
||||
,COUNT(*) AS DRUG_EXPOSURE_COUNT
|
||||
,30 AS gap_days
|
||||
FROM #cteDrugExpEnds
|
||||
GROUP BY person_id
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,drug_type_concept_id
|
||||
,ERA_END_DATE;
|
||||
</code></pre>
|
||||
INSERT INTO @cdm_schema.drug_era(drug_era_id,person_id, drug_concept_id, drug_era_start_date, drug_era_end_date, drug_exposure_count, gap_days)
|
||||
SELECT * FROM #tmp_de;</code></pre>
|
||||
</div>
|
||||
</div>
|
||||
<div id="example-etl-script" class="section level2">
|
||||
|
|
|
|||
|
|
@ -0,0 +1,469 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>Local Data</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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 -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<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-home"></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>
|
||||
</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">Local Data</h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>Okay, so you don’t have a network use case. <strong>Is this data element specific to your data source, or are there others in the community who might also have this data but don’t yet need it for a study or data model convention?</strong></p>
|
||||
<p><a href="localChange.html">Yes, this element is specific to my data source</a></p>
|
||||
<p><a href="leaveAsIs.html">No, there are others in the community who also have this data</a></p>
|
||||
|
||||
|
||||
|
||||
|
||||
</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 -->
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
@ -0,0 +1,470 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>OMOP Vocabulary</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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 -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<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-home"></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>
|
||||
</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">OMOP Vocabulary</h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>Great, you have a network use case!</p>
|
||||
<p>Next question: <strong>Is there an existing OMOP vocabulary to support this new element? If you are unsure, feel free to check <a href="https://athena.ohdsi.org/search-terms/terms?query">Athena</a>.</strong></p>
|
||||
<p><a href="vocabY.html">Yes, I have all the required vocabulary I need</a></p>
|
||||
<p><a href="vocabN.html">No, I there is not an existing OMOP vocabulary to support my request</a></p>
|
||||
|
||||
|
||||
|
||||
|
||||
</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 -->
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
@ -0,0 +1,469 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>Open Source Vocabulary</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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 -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<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-home"></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>
|
||||
</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">Open Source Vocabulary</h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>Okay, so you have a use case but you don’t have an OMOP vocabulary to support your need. <strong>Is there an existing open-source (not proprietary or custom) vocabulary that has not yet been incorporated into the OMOP vocabulary?</strong></p>
|
||||
<p><a href="vocabRequest.html">Yes, the vocabulary exists, it just needs to be brought in</a></p>
|
||||
<p><a href="contactVocab.html">No, there is no open-source vocabulary for this data element</a></p>
|
||||
|
||||
|
||||
|
||||
|
||||
</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 -->
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
@ -0,0 +1,469 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>Vocabulary Request</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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 -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<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-home"></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>
|
||||
</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">Vocabulary Request</h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>Okay so you have something you would like to add to the CDM and there is an existing OMOP vocabulary we can bring in to support it. <strong>In this case, please open an issue on the vocabulary github with the details of what you need added</strong> as data elements in the CDM must have a vocabulary in place before they can be implemented. The team will follow up with you should they need additional information.</p>
|
||||
<p><a href="https://github.com/OHDSI/Vocabulary-v5.0/issues">Vocabulary GitHub Issue Tracker</a></p>
|
||||
<p>Once that request is made, please follow the <a href="cdmRequestProcess.html">CDM Request Process</a> to begin the steps soliciting a change or addition to the model itself. Need more guidance? Consider contacting the CDM Working Group on our <a href="https://github.com/OHDSI/CommonDataModel">GitHub</a> or <a href="https://teams.microsoft.com/l/team/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/conversations?groupId=a6f2c516-e568-4974-8f1e-a7bdc2f997c5&tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5">Teams Channel</a>.</p>
|
||||
|
||||
|
||||
|
||||
|
||||
</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 -->
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
@ -0,0 +1,468 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>Request Process</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.13/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/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 it active
|
||||
menuAnchor.tab('show');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.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 {
|
||||
content: "";
|
||||
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: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.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 -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<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-home"></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>
|
||||
</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">Request Process</h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>Great, so you have a network use case and an existing OMOP Vocabulary! <strong>From here, please follow the steps to formally request a change to the OMOP Common Data Model.</strong></p>
|
||||
<p><a href="cdmRequestProcess.html">CDM Request Process</a></p>
|
||||
|
||||
|
||||
|
||||
|
||||
</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 -->
|
||||
|
||||
|
||||
<!-- 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>
|
||||
|
|
@ -13,7 +13,7 @@
|
|||
|
||||
<title>How the Vocabulary is Built</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
|
||||
<script src="site_libs/header-attrs-2.13/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" />
|
||||
|
|
@ -63,6 +63,7 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
details > summary > p:only-child {
|
||||
display: inline;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
|
|
@ -312,7 +316,7 @@ div.tocify {
|
|||
<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-target="#navbar">
|
||||
<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>
|
||||
|
|
@ -328,7 +332,7 @@ div.tocify {
|
|||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
|
@ -348,7 +352,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -368,7 +372,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -386,7 +390,7 @@ div.tocify {
|
|||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<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>
|
||||
|
|
@ -399,19 +403,22 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
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" aria-expanded="false">Accepted</a>
|
||||
<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>
|
||||
|
|
@ -421,7 +428,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -441,7 +448,7 @@ div.tocify {
|
|||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<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
|
||||
|
|
@ -449,6 +456,9 @@ div.tocify {
|
|||
<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>
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
cdmTableName,schema,isRequired,conceptPrefix,measurePersonCompleteness,measurePersonCompletenessThreshold,validation,tableDescription,userGuidance,etlConventions
|
||||
PERSON,CDM,Yes,,No,,,"This table serves as the central identity management for all Persons in the database. It contains records that uniquely identify each person or patient, and some demographic information. ",All records in this table are independent Persons.,"All Persons in a database needs one record in this table, unless they fail data quality requirements specified in the ETL. Persons with no Events should have a record nonetheless. If more than one data source contributes Events to the database, Persons must be reconciled, if possible, across the sources to create one single record per Person. The content of the BIRTH_DATETIME must be equivalent to the content of BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR. "
|
||||
OBSERVATION_PERIOD,CDM,Yes,,Yes,0,,"This table contains records which define spans of time during which two conditions are expected to hold: (i) Clinical Events that happened to the Person are recorded in the Event tables, and (ii) absense of records indicate such Events did not occur during this span of time.","For each Person, one or more OBSERVATION_PERIOD records may be present, but they will not overlap or be back to back to each other. Events may exist outside all of the time spans of the OBSERVATION_PERIOD records for a patient, however, absence of an Event outside these time spans cannot be construed as evidence of absence of an Event. Incidence or prevalence rates should only be calculated for the time of active OBSERVATION_PERIOD records. When constructing cohorts, outside Events can be used for inclusion criteria definition, but without any guarantee for the performance of these criteria. Also, OBSERVATION_PERIOD records can be as short as a single day, greatly disturbing the denominator of any rate calculation as part of cohort characterizations. To avoid that, apply minimal observation time as a requirement for any cohort definition.","Each Person needs to have at least one OBSERVATION_PERIOD record, which should represent time intervals with a high capture rate of Clinical Events. Some source data have very similar concepts, such as enrollment periods in insurance claims data. In other source data such as most EHR systems these time spans need to be inferred under a set of assumptions. It is the discretion of the ETL developer to define these assumptions. In many ETL solutions the start date of the first occurrence or the first high quality occurrence of a Clinical Event (Condition, Drug, Procedure, Device, Measurement, Visit) is defined as the start of the OBSERVATION_PERIOD record, and the end date of the last occurrence of last high quality occurrence of a Clinical Event, or the end of the database period becomes the end of the OBSERVATOIN_PERIOD for each Person. If a Person only has a single Clinical Event the OBSERVATION_PERIOD record can be as short as one day. Depending on these definitions it is possible that Clinical Events fall outside the time spans defined by OBSERVATION_PERIOD records. Family history or history of Clinical Events generally are not used to generate OBSERVATION_PERIOD records around the time they are referring to. Any two overlapping or adjacent OBSERVATION_PERIOD records have to be merged into one."
|
||||
cdmTableName,schema,isRequired,conceptPrefix,measurePersonCompleteness,measurePersonCompletenessThreshold,validation,tableDescription,userGuidance,etlConventions
|
||||
PERSON,CDM,Yes,,No,,,"This table serves as the central identity management for all Persons in the database. It contains records that uniquely identify each person or patient, and some demographic information. ",All records in this table are independent Persons.,"All Persons in a database needs one record in this table, unless they fail data quality requirements specified in the ETL. Persons with no Events should have a record nonetheless. If more than one data source contributes Events to the database, Persons must be reconciled, if possible, across the sources to create one single record per Person. The content of the BIRTH_DATETIME must be equivalent to the content of BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR. "
|
||||
OBSERVATION_PERIOD,CDM,Yes,,Yes,0,,"This table contains records which define spans of time during which two conditions are expected to hold: (i) Clinical Events that happened to the Person are recorded in the Event tables, and (ii) absense of records indicate such Events did not occur during this span of time.","For each Person, one or more OBSERVATION_PERIOD records may be present, but they will not overlap or be back to back to each other. Events may exist outside all of the time spans of the OBSERVATION_PERIOD records for a patient, however, absence of an Event outside these time spans cannot be construed as evidence of absence of an Event. Incidence or prevalence rates should only be calculated for the time of active OBSERVATION_PERIOD records. When constructing cohorts, outside Events can be used for inclusion criteria definition, but without any guarantee for the performance of these criteria. Also, OBSERVATION_PERIOD records can be as short as a single day, greatly disturbing the denominator of any rate calculation as part of cohort characterizations. To avoid that, apply minimal observation time as a requirement for any cohort definition.","Each Person needs to have at least one OBSERVATION_PERIOD record, which should represent time intervals with a high capture rate of Clinical Events. Some source data have very similar concepts, such as enrollment periods in insurance claims data. In other source data such as most EHR systems these time spans need to be inferred under a set of assumptions. It is the discretion of the ETL developer to define these assumptions. In many ETL solutions the start date of the first occurrence or the first high quality occurrence of a Clinical Event (Condition, Drug, Procedure, Device, Measurement, Visit) is defined as the start of the OBSERVATION_PERIOD record, and the end date of the last occurrence of last high quality occurrence of a Clinical Event, or the end of the database period becomes the end of the OBSERVATOIN_PERIOD for each Person. If a Person only has a single Clinical Event the OBSERVATION_PERIOD record can be as short as one day. Depending on these definitions it is possible that Clinical Events fall outside the time spans defined by OBSERVATION_PERIOD records. Family history or history of Clinical Events generally are not used to generate OBSERVATION_PERIOD records around the time they are referring to. Any two overlapping or adjacent OBSERVATION_PERIOD records have to be merged into one."
|
||||
VISIT_OCCURRENCE,CDM,No,VISIT_,Yes,0,,"This table contains Events where Persons engage with the healthcare system for a duration of time. They are often also called ""Encounters"". Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. ","The configuration defining the Visit are described by Concepts in the Visit Domain, which form a hierarchical structure, but rolling up to generally familiar Visits adopted in most healthcare systems worldwide:
|
||||
|
||||
- [Inpatient Visit](https://athena.ohdsi.org/search-terms/terms/9201): Person visiting hospital, at a Care Site, in bed, for duration of more than one day, with physicians and other Providers permanently available to deliver service around the clock
|
||||
|
|
@ -15,15 +15,15 @@ VISIT_OCCURRENCE,CDM,No,VISIT_,Yes,0,,"This table contains Events where Persons
|
|||
- [Ambulance Visit](https://athena.ohdsi.org/search-terms/terms/581478): Person using transportation service for the purpose of initiating one of the other Visits, without a Care Site, within one day, potentially with Providers accompanying the Visit and delivering service
|
||||
- [Case Management Visit](https://athena.ohdsi.org/search-terms/terms/38004193): Person interacting with healthcare system, without a Care Site, within a day, with no Providers involved, for administrative purposes
|
||||
|
||||
The Visit duration, or 'length of stay', is defined as VISIT_END_DATE - VISIT_START_DATE. For all Visits this is <1 day, except Inpatient Visits and Non-hospital institution Visits. The CDM also contains the VISIT_DETAIL table where additional information about the Visit is stored, for example, transfers between units during an inpatient Visit.","Visits can be derived easily if the source data contain coding systems for Place of Service or Procedures, like CPT codes for well visits. In those cases, the codes can be looked up and mapped to a Standard Visit Concept. Otherwise, Visit Concepts have to be identified in the ETL process. This table will contain concepts in the Visit domain. These concepts are arranged in a hierarchical structure to facilitate cohort definitions by rolling up to generally familiar Visits adopted in most healthcare systems worldwide. Visits can be adjacent to each other, i.e. the end date of one can be identical with the start date of the other. As a consequence, more than one-day Visits or their descendants can be recorded for the same day. Multi-day visits must not overlap, i.e. share days other than start and end days. It is often the case that some logic should be written for how to define visits and how to assign Visit_Concept_Id. For example, in US claims outpatient visits that appear to occur within the time period of an inpatient visit can be rolled into one with the same Visit_Occurrence_Id. In EHR data inpatient visits that are within one day of each other may be strung together to create one visit. It will all depend on the source data and how encounter records should be translated to visit occurrences. Providers can be associated with a Visit through the PROVIDER_ID field, or indirectly through PROCEDURE_OCCURRENCE records linked both to the VISIT and PROVIDER tables."
|
||||
VISIT_DETAIL,CDM,No,VISIT_DETAIL_,Yes,0,,The VISIT_DETAIL table is an optional table used to represents details of each record in the parent VISIT_OCCURRENCE table. A good example of this would be the movement between units in a hospital during an inpatient stay or claim lines associated with a one insurance claim. For every record in the VISIT_OCCURRENCE table there may be 0 or more records in the VISIT_DETAIL table with a 1:n relationship where n may be 0. The VISIT_DETAIL table is structurally very similar to VISIT_OCCURRENCE table and belongs to the visit domain.,"The configuration defining the Visit Detail is described by Concepts in the Visit Domain, which form a hierarchical structure. The Visit Detail record will have an associated to the Visit Occurrence record in two ways: <br> 1. The Visit Detail record will have the VISIT_OCCURRENCE_ID it is associated to 2. The VISIT_DETAIL_CONCEPT_ID will be a descendant of the VISIT_CONCEPT_ID for the Visit.","It is not mandatory that the VISIT_DETAIL table be filled in, but if you find that the logic to create VISIT_OCCURRENCE records includes the roll-up of multiple smaller records to create one picture of a Visit then it is a good idea to use VISIT_DETAIL. In EHR data, for example, a Person may be in the hospital but instead of one over-arching Visit their encounters are recorded as times they interacted with a health care provider. A Person in the hospital interacts with multiple providers multiple times a day so the encounters must be strung together using some heuristic (defined by the ETL) to identify the entire Visit. In this case the encounters would be considered Visit Details and the entire Visit would be the Visit Occurrence. In this example it is also possible to use the Vocabulary to distinguish Visit Details from a Visit Occurrence by setting the VISIT_CONCEPT_ID to [9201](https://athena.ohdsi.org/search-terms/terms/9201) and the VISIT_DETAIL_CONCEPT_IDs either to 9201 or its children to indicate where the patient was in the hospital at the time of care."
|
||||
CONDITION_OCCURRENCE,CDM,No,CONDITION_,Yes,0,,"This table contains records of Events of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign, or a symptom, which is either observed by a Provider or reported by the patient. ","Conditions are defined by Concepts from the Condition domain, which form a complex hierarchy. As a result, the same Person with the same disease may have multiple Condition records, which belong to the same hierarchical family. Most Condition records are mapped from diagnostic codes, but recorded signs, symptoms and summary descriptions also contribute to this table. Rule out diagnoses should not be recorded in this table, but in reality their negating nature is not always captured in the source data, and other precautions must be taken when when identifying Persons who should suffer from the recorded Condition. Record all conditions as they exist in the source data. Any decisions about diagnosis/phenotype definitions would be done through cohort specifications. These cohorts can be housed in the [COHORT](https://ohdsi.github.io/CommonDataModel/cdm531.html#payer_plan_period) table. Conditions span a time interval from start to end, but are typically recorded as single snapshot records with no end date. The reason is twofold: (i) At the time of the recording the duration is not known and later not recorded, and (ii) the Persons typically cease interacting with the healthcare system when they feel better, which leads to incomplete capture of resolved Conditions. The [CONDITION_ERA](https://ohdsi.github.io/CommonDataModel/cdm531.html#condition_era) table addresses this issue. Family history and past diagnoses ('history of') are not recorded in this table. Instead, they are listed in the [OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table. Codes written in the process of establishing the diagnosis, such as 'question of' of and 'rule out', should not represented here. Instead, they should be recorded in the [OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table, if they are used for analyses. However, this information is not always available.",Source codes and source text fields mapped to Standard Concepts of the Condition Domain have to be recorded here.
|
||||
DRUG_EXPOSURE,CDM,No,DRUG_,Yes,0,,"This table captures records about the exposure to a Drug ingested or otherwise introduced into the body. A Drug is a biochemical substance formulated in such a way that when administered to a Person it will exert a certain biochemical effect on the metabolism. Drugs include prescription and over-the-counter medicines, vaccines, and large-molecule biologic therapies. Radiological devices ingested or applied locally do not count as Drugs.","The purpose of records in this table is to indicate an exposure to a certain drug as best as possible. In this context a drug is defined as an active ingredient. Drug Exposures are defined by Concepts from the Drug domain, which form a complex hierarchy. As a result, one DRUG_SOURCE_CONCEPT_ID may map to multiple standard concept ids if it is a combination product. Records in this table represent prescriptions written, prescriptions dispensed, and drugs administered by a provider to name a few. The DRUG_TYPE_CONCEPT_ID can be used to find and filter on these types. This table includes additional information about the drug products, the quantity given, and route of administration.",Information about quantity and dose is provided in a variety of different ways and it is important for the ETL to provide as much information as possible from the data. Depending on the provenance of the data fields may be captured differently i.e. quantity for drugs administered may have a separate meaning from quantity for prescriptions dispensed. If a patient has multiple records on the same day for the same drug or procedures the ETL should not de-dupe them unless there is probable reason to believe the item is a true data duplicate. Take note on how to handle refills for prescriptions written.
|
||||
PROCEDURE_OCCURRENCE,CDM,No,PROCEDURE_,Yes,0,,"This table contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient with a diagnostic or therapeutic purpose.","Lab tests are not a procedure, if something is observed with an expected resulting amount and unit then it should be a measurement. Phlebotomy is a procedure but so trivial that it tends to be rarely captured. It can be assumed that there is a phlebotomy procedure associated with many lab tests, therefore it is unnecessary to add them as separate procedures. If the user finds the same procedure over concurrent days, it is assumed those records are part of a procedure lasting more than a day. This logic is in lieu of the procedure_end_date, which will be added in a future version of the CDM.","If a procedure lasts more than a day, then it should be recorded as a separate record for each day the procedure occurred, this logic is in lieu of the PROCEDURE_END_DATE, which will be added in a future version of the CDM. When dealing with duplicate records, the ETL must determine whether to sum them up into one record or keep them separate. Things to consider are: - Same Procedure - Same PROCEDURE_DATETIME - Same Visit Occurrence or Visit Detail - Same Provider - Same Modifier for Procedures. Source codes and source text fields mapped to Standard Concepts of the Procedure Domain have to be recorded here."
|
||||
DEVICE_EXPOSURE,CDM,No,DEVICE_,Yes,0,,"The Device domain captures information about a person's exposure to a foreign physical object or instrument which is used for diagnostic or therapeutic purposes through a mechanism beyond chemical action. Devices include implantable objects (e.g. pacemakers, stents, artificial joints), medical equipment and supplies (e.g. bandages, crutches, syringes), other instruments used in medical procedures (e.g. sutures, defibrillators) and material used in clinical care (e.g. adhesives, body material, dental material, surgical material).","The distinction between Devices or supplies and Procedures are sometimes blurry, but the former are physical objects while the latter are actions, often to apply a Device or supply.",Source codes and source text fields mapped to Standard Concepts of the Device Domain have to be recorded here.
|
||||
MEASUREMENT,CDM,No,MEASUREMENT_,Yes,0,,"The MEASUREMENT table contains records of Measurements, i.e. structured values (numerical or categorical) obtained through systematic and standardized examination or testing of a Person or Person's sample. The MEASUREMENT table contains both orders and results of such Measurements as laboratory tests, vital signs, quantitative findings from pathology reports, etc. Measurements are stored as attribute value pairs, with the attribute as the Measurement Concept and the value representing the result. The value can be a Concept (stored in VALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with a Unit (UNIT_CONCEPT_ID). The Procedure for obtaining the sample is housed in the PROCEDURE_OCCURRENCE table, though it is unnecessary to create a PROCEDURE_OCCURRENCE record for each measurement if one does not exist in the source data. Measurements differ from Observations in that they require a standardized test or some other activity to generate a quantitative or qualitative result. If there is no result, it is assumed that the lab test was conducted but the result was not captured.","Measurements are predominately lab tests with a few exceptions, like blood pressure or function tests. Results are given in the form of a value and unit combination. When investigating measurements, look for operator_concept_ids (<, >, etc.).","Only records where the source value maps to a Concept in the measurement domain should be included in this table. Even though each Measurement always has a result, the fields VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are not mandatory as often the result is not given in the source data. When the result is not known, the Measurement record represents just the fact that the corresponding Measurement was carried out, which in itself is already useful information for some use cases. For some Measurement Concepts, the result is included in the test. For example, ICD10 CONCEPT_ID [45548980](https://athena.ohdsi.org/search-terms/terms/45548980) 'Abnormal level of unspecified serum enzyme' indicates a Measurement and the result (abnormal). In those situations, the CONCEPT_RELATIONSHIP table in addition to the 'Maps to' record contains a second record with the relationship_id set to 'Maps to value'. In this example, the 'Maps to' relationship directs to [4046263](https://athena.ohdsi.org/search-terms/terms/4046263) 'Enzyme measurement' as well as a 'Maps to value' record to [4135493](https://athena.ohdsi.org/search-terms/terms/4135493) 'Abnormal'."
|
||||
OBSERVATION,CDM,No,OBSERVATION_,Yes,0,,"The OBSERVATION table captures clinical facts about a Person obtained in the context of examination, questioning or a procedure. Any data that cannot be represented by any other domains, such as social and lifestyle facts, medical history, family history, etc. are recorded here.","Observations differ from Measurements in that they do not require a standardized test or some other activity to generate clinical fact. Typical observations are medical history, family history, the stated need for certain treatment, social circumstances, lifestyle choices, healthcare utilization patterns, etc. If the generation clinical facts requires a standardized testing such as lab testing or imaging and leads to a standardized result, the data item is recorded in the MEASUREMENT table. If the clinical fact observed determines a sign, symptom, diagnosis of a disease or other medical condition, it is recorded in the CONDITION_OCCURRENCE table. Valid Observation Concepts are not enforced to be from any domain though they still should be Standard Concepts.","Records whose Source Values map to any domain besides Condition, Procedure, Drug, Measurement or Device should be stored in the Observation table. Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be a Concept (stored in VALUE_AS_CONCEPT), a numerical value (VALUE_AS_NUMBER), a verbatim string (VALUE_AS_STRING), or a datetime (VALUE_AS_DATETIME). Even though Observations do not have an explicit result, the clinical fact can be stated separately from the type of Observation in the VALUE_AS_* fields. It is recommended for Observations that are suggestive statements of positive assertion should have a value of 'Yes' (concept_id=4188539), recorded, even though the null value is the equivalent. "
|
||||
DEATH,CDM,No,,No,,,"The death domain contains the clinical event for how and when a Person dies. A person can have up to one record if the source system contains evidence about the Death, such as: Condition in an administrative claim, status of enrollment into a health plan, or explicit record in EHR data.",,
|
||||
The Visit duration, or 'length of stay', is defined as VISIT_END_DATE - VISIT_START_DATE. For all Visits this is <1 day, except Inpatient Visits and Non-hospital institution Visits. The CDM also contains the VISIT_DETAIL table where additional information about the Visit is stored, for example, transfers between units during an inpatient Visit.","Visits can be derived easily if the source data contain coding systems for Place of Service or Procedures, like CPT codes for well visits. In those cases, the codes can be looked up and mapped to a Standard Visit Concept. Otherwise, Visit Concepts have to be identified in the ETL process. This table will contain concepts in the Visit domain. These concepts are arranged in a hierarchical structure to facilitate cohort definitions by rolling up to generally familiar Visits adopted in most healthcare systems worldwide. Visits can be adjacent to each other, i.e. the end date of one can be identical with the start date of the other. As a consequence, more than one-day Visits or their descendants can be recorded for the same day. Multi-day visits must not overlap, i.e. share days other than start and end days. It is often the case that some logic should be written for how to define visits and how to assign Visit_Concept_Id. For example, in US claims outpatient visits that appear to occur within the time period of an inpatient visit can be rolled into one with the same Visit_Occurrence_Id. In EHR data inpatient visits that are within one day of each other may be strung together to create one visit. It will all depend on the source data and how encounter records should be translated to visit occurrences. Providers can be associated with a Visit through the PROVIDER_ID field, or indirectly through PROCEDURE_OCCURRENCE records linked both to the VISIT and PROVIDER tables."
|
||||
VISIT_DETAIL,CDM,No,VISIT_DETAIL_,Yes,0,,The VISIT_DETAIL table is an optional table used to represents details of each record in the parent VISIT_OCCURRENCE table. A good example of this would be the movement between units in a hospital during an inpatient stay or claim lines associated with a one insurance claim. For every record in the VISIT_OCCURRENCE table there may be 0 or more records in the VISIT_DETAIL table with a 1:n relationship where n may be 0. The VISIT_DETAIL table is structurally very similar to VISIT_OCCURRENCE table and belongs to the visit domain.,"The configuration defining the Visit Detail is described by Concepts in the Visit Domain, which form a hierarchical structure. The Visit Detail record will have an associated to the Visit Occurrence record in two ways: <br> 1. The Visit Detail record will have the VISIT_OCCURRENCE_ID it is associated to 2. The VISIT_DETAIL_CONCEPT_ID will be a descendant of the VISIT_CONCEPT_ID for the Visit.","It is not mandatory that the VISIT_DETAIL table be filled in, but if you find that the logic to create VISIT_OCCURRENCE records includes the roll-up of multiple smaller records to create one picture of a Visit then it is a good idea to use VISIT_DETAIL. In EHR data, for example, a Person may be in the hospital but instead of one over-arching Visit their encounters are recorded as times they interacted with a health care provider. A Person in the hospital interacts with multiple providers multiple times a day so the encounters must be strung together using some heuristic (defined by the ETL) to identify the entire Visit. In this case the encounters would be considered Visit Details and the entire Visit would be the Visit Occurrence. In this example it is also possible to use the Vocabulary to distinguish Visit Details from a Visit Occurrence by setting the VISIT_CONCEPT_ID to [9201](https://athena.ohdsi.org/search-terms/terms/9201) and the VISIT_DETAIL_CONCEPT_IDs either to 9201 or its children to indicate where the patient was in the hospital at the time of care."
|
||||
CONDITION_OCCURRENCE,CDM,No,CONDITION_,Yes,0,,"This table contains records of Events of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign, or a symptom, which is either observed by a Provider or reported by the patient. ","Conditions are defined by Concepts from the Condition domain, which form a complex hierarchy. As a result, the same Person with the same disease may have multiple Condition records, which belong to the same hierarchical family. Most Condition records are mapped from diagnostic codes, but recorded signs, symptoms and summary descriptions also contribute to this table. Rule out diagnoses should not be recorded in this table, but in reality their negating nature is not always captured in the source data, and other precautions must be taken when when identifying Persons who should suffer from the recorded Condition. Record all conditions as they exist in the source data. Any decisions about diagnosis/phenotype definitions would be done through cohort specifications. These cohorts can be housed in the [COHORT](https://ohdsi.github.io/CommonDataModel/cdm531.html#payer_plan_period) table. Conditions span a time interval from start to end, but are typically recorded as single snapshot records with no end date. The reason is twofold: (i) At the time of the recording the duration is not known and later not recorded, and (ii) the Persons typically cease interacting with the healthcare system when they feel better, which leads to incomplete capture of resolved Conditions. The [CONDITION_ERA](https://ohdsi.github.io/CommonDataModel/cdm531.html#condition_era) table addresses this issue. Family history and past diagnoses ('history of') are not recorded in this table. Instead, they are listed in the [OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table. Codes written in the process of establishing the diagnosis, such as 'question of' of and 'rule out', should not represented here. Instead, they should be recorded in the [OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table, if they are used for analyses. However, this information is not always available.",Source codes and source text fields mapped to Standard Concepts of the Condition Domain have to be recorded here.
|
||||
DRUG_EXPOSURE,CDM,No,DRUG_,Yes,0,,"This table captures records about the exposure to a Drug ingested or otherwise introduced into the body. A Drug is a biochemical substance formulated in such a way that when administered to a Person it will exert a certain biochemical effect on the metabolism. Drugs include prescription and over-the-counter medicines, vaccines, and large-molecule biologic therapies. Radiological devices ingested or applied locally do not count as Drugs.","The purpose of records in this table is to indicate an exposure to a certain drug as best as possible. In this context a drug is defined as an active ingredient. Drug Exposures are defined by Concepts from the Drug domain, which form a complex hierarchy. As a result, one DRUG_SOURCE_CONCEPT_ID may map to multiple standard concept ids if it is a combination product. Records in this table represent prescriptions written, prescriptions dispensed, and drugs administered by a provider to name a few. The DRUG_TYPE_CONCEPT_ID can be used to find and filter on these types. This table includes additional information about the drug products, the quantity given, and route of administration.",Information about quantity and dose is provided in a variety of different ways and it is important for the ETL to provide as much information as possible from the data. Depending on the provenance of the data fields may be captured differently i.e. quantity for drugs administered may have a separate meaning from quantity for prescriptions dispensed. If a patient has multiple records on the same day for the same drug or procedures the ETL should not de-dupe them unless there is probable reason to believe the item is a true data duplicate. Take note on how to handle refills for prescriptions written.
|
||||
PROCEDURE_OCCURRENCE,CDM,No,PROCEDURE_,Yes,0,,"This table contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient with a diagnostic or therapeutic purpose.","Lab tests are not a procedure, if something is observed with an expected resulting amount and unit then it should be a measurement. Phlebotomy is a procedure but so trivial that it tends to be rarely captured. It can be assumed that there is a phlebotomy procedure associated with many lab tests, therefore it is unnecessary to add them as separate procedures. If the user finds the same procedure over concurrent days, it is assumed those records are part of a procedure lasting more than a day. This logic is in lieu of the procedure_end_date, which will be added in a future version of the CDM.","If a procedure lasts more than 24 hours, then it should be recorded as a separate record for each day the procedure occurred, this logic is in lieu of the PROCEDURE_END_DATE, which will be added in a future version of the CDM. When dealing with duplicate records, the ETL must determine whether to sum them up into one record or keep them separate. Things to consider are: - Same Procedure - Same PROCEDURE_DATETIME - Same Visit Occurrence or Visit Detail - Same Provider - Same Modifier for Procedures. Source codes and source text fields mapped to Standard Concepts of the Procedure Domain have to be recorded here."
|
||||
DEVICE_EXPOSURE,CDM,No,DEVICE_,Yes,0,,"The Device domain captures information about a person's exposure to a foreign physical object or instrument which is used for diagnostic or therapeutic purposes through a mechanism beyond chemical action. Devices include implantable objects (e.g. pacemakers, stents, artificial joints), medical equipment and supplies (e.g. bandages, crutches, syringes), other instruments used in medical procedures (e.g. sutures, defibrillators) and material used in clinical care (e.g. adhesives, body material, dental material, surgical material).","The distinction between Devices or supplies and Procedures are sometimes blurry, but the former are physical objects while the latter are actions, often to apply a Device or supply.",Source codes and source text fields mapped to Standard Concepts of the Device Domain have to be recorded here.
|
||||
MEASUREMENT,CDM,No,MEASUREMENT_,Yes,0,,"The MEASUREMENT table contains records of Measurements, i.e. structured values (numerical or categorical) obtained through systematic and standardized examination or testing of a Person or Person's sample. The MEASUREMENT table contains both orders and results of such Measurements as laboratory tests, vital signs, quantitative findings from pathology reports, etc. Measurements are stored as attribute value pairs, with the attribute as the Measurement Concept and the value representing the result. The value can be a Concept (stored in VALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with a Unit (UNIT_CONCEPT_ID). The Procedure for obtaining the sample is housed in the PROCEDURE_OCCURRENCE table, though it is unnecessary to create a PROCEDURE_OCCURRENCE record for each measurement if one does not exist in the source data. Measurements differ from Observations in that they require a standardized test or some other activity to generate a quantitative or qualitative result. If there is no result, it is assumed that the lab test was conducted but the result was not captured.","Measurements are predominately lab tests with a few exceptions, like blood pressure or function tests. Results are given in the form of a value and unit combination. When investigating measurements, look for operator_concept_ids (<, >, etc.).","Only records where the source value maps to a Concept in the measurement domain should be included in this table. Even though each Measurement always has a result, the fields VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are not mandatory as often the result is not given in the source data. When the result is not known, the Measurement record represents just the fact that the corresponding Measurement was carried out, which in itself is already useful information for some use cases. For some Measurement Concepts, the result is included in the test. For example, ICD10 CONCEPT_ID [45548980](https://athena.ohdsi.org/search-terms/terms/45548980) 'Abnormal level of unspecified serum enzyme' indicates a Measurement and the result (abnormal). In those situations, the CONCEPT_RELATIONSHIP table in addition to the 'Maps to' record contains a second record with the relationship_id set to 'Maps to value'. In this example, the 'Maps to' relationship directs to [4046263](https://athena.ohdsi.org/search-terms/terms/4046263) 'Enzyme measurement' as well as a 'Maps to value' record to [4135493](https://athena.ohdsi.org/search-terms/terms/4135493) 'Abnormal'."
|
||||
OBSERVATION,CDM,No,OBSERVATION_,Yes,0,,"The OBSERVATION table captures clinical facts about a Person obtained in the context of examination, questioning or a procedure. Any data that cannot be represented by any other domains, such as social and lifestyle facts, medical history, family history, etc. are recorded here.","Observations differ from Measurements in that they do not require a standardized test or some other activity to generate clinical fact. Typical observations are medical history, family history, the stated need for certain treatment, social circumstances, lifestyle choices, healthcare utilization patterns, etc. If the generation clinical facts requires a standardized testing such as lab testing or imaging and leads to a standardized result, the data item is recorded in the MEASUREMENT table. If the clinical fact observed determines a sign, symptom, diagnosis of a disease or other medical condition, it is recorded in the CONDITION_OCCURRENCE table. Valid Observation Concepts are not enforced to be from any domain though they still should be Standard Concepts.","Records whose Source Values map to any domain besides Condition, Procedure, Drug, Measurement or Device should be stored in the Observation table. Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be a Concept (stored in VALUE_AS_CONCEPT), a numerical value (VALUE_AS_NUMBER), a verbatim string (VALUE_AS_STRING), or a datetime (VALUE_AS_DATETIME). Even though Observations do not have an explicit result, the clinical fact can be stated separately from the type of Observation in the VALUE_AS_* fields. It is recommended for Observations that are suggestive statements of positive assertion should have a value of 'Yes' (concept_id=4188539), recorded, even though the null value is the equivalent. "
|
||||
DEATH,CDM,No,,No,,,"The death domain contains the clinical event for how and when a Person dies. A person can have up to one record if the source system contains evidence about the Death, such as: Condition in an administrative claim, status of enrollment into a health plan, or explicit record in EHR data.",,
|
||||
NOTE,CDM,No,,Yes,0,,"The NOTE table captures unstructured information that was recorded by a provider about a patient in free text (in ASCII, or preferably in UTF8 format) notes on a given date. The type of note_text is CLOB or varchar(MAX) depending on RDBMS. ",,"HL7/LOINC CDO is a standard for consistent naming of documents to support a range of use cases: retrieval, organization, display, and exchange. It guides the creation of LOINC codes for clinical notes. CDO annotates each document with 5 dimensions:
|
||||
|
||||
- **Kind of Document**: Characterizes the general structure of the document at a macro level (e.g. Anesthesia Consent)
|
||||
|
|
@ -34,21 +34,21 @@ NOTE,CDM,No,,Yes,0,,"The NOTE table captures unstructured information that was r
|
|||
Each combination of these 5 dimensions rolls up to a unique LOINC code.
|
||||
|
||||
According to CDO requirements, only 2 of the 5 dimensions are required to properly annotate a document; Kind of Document and any one of the other 4 dimensions.
|
||||
However, not all the permutations of the CDO dimensions will necessarily yield an existing LOINC code. Each of these dimensions are contained in the OMOP Vocabulary under the domain of 'Meas Value' with each dimension represented as a Concept Class. "
|
||||
NOTE_NLP,CDM,No,,No,,,The NOTE_NLP table encodes all output of NLP on clinical notes. Each row represents a single extracted term from a note.,,
|
||||
SPECIMEN,CDM,No,SPECIMEN_,Yes,0,,The specimen domain contains the records identifying biological samples from a person.,,"Anatomic site is coded at the most specific level of granularity possible, such that higher level classifications can be derived using the Standardized Vocabularies."
|
||||
However, not all the permutations of the CDO dimensions will necessarily yield an existing LOINC code. Each of these dimensions are contained in the OMOP Vocabulary under the domain of 'Meas Value' with each dimension represented as a Concept Class. "
|
||||
NOTE_NLP,CDM,No,,No,,,The NOTE_NLP table encodes all output of NLP on clinical notes. Each row represents a single extracted term from a note.,,
|
||||
SPECIMEN,CDM,No,SPECIMEN_,Yes,0,,The specimen domain contains the records identifying biological samples from a person.,,"Anatomic site is coded at the most specific level of granularity possible, such that higher level classifications can be derived using the Standardized Vocabularies."
|
||||
FACT_RELATIONSHIP,CDM,No,,No,,,"The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the CDM. Relationships can be defined between facts from the same domain, or different domains. Examples of Fact Relationships include: [Person relationships](https://athena.ohdsi.org/search-terms/terms?domain=Relationship&standardConcept=Standard&page=2&pageSize=15&query=) (parent-child), care site relationships (hierarchical organizational structure of facilities within a health system), indication relationship (between drug exposures and associated conditions), usage relationships (of devices during the course of an associated procedure), or facts derived from one another (measurements derived from an associated specimen).",,"All relationships are directional, and each relationship is represented twice symmetrically within the FACT_RELATIONSHIP table. For example, two persons if person_id = 1 is the mother of person_id = 2 two records are in the FACT_RELATIONSHIP table (all strings in fact concept_id records in the Concept table:
|
||||
- Person, 1, Person, 2, parent of
|
||||
- Person, 2, Person, 1, child of"
|
||||
LOCATION,CDM,No,,No,,,The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites.,,"Each address or Location is unique and is present only once in the table. Locations do not contain names, such as the name of a hospital. In order to construct a full address that can be used in the postal service, the address information from the Location needs to be combined with information from the Care Site."
|
||||
CARE_SITE,CDM,No,,No,,,"The CARE_SITE table contains a list of uniquely identified institutional (physical or organizational) units where healthcare delivery is practiced (offices, wards, hospitals, clinics, etc.).",,"Care site is a unique combination of location_id and place_of_service_source_value. Care site does not take into account the provider (human) information such a specialty. Many source data do not make a distinction between individual and institutional providers. The CARE_SITE table contains the institutional providers. If the source, instead of uniquely identifying individual Care Sites, only provides limited information such as Place of Service, generic or ""pooled"" Care Site records are listed in the CARE_SITE table. There can be hierarchical and business relationships between Care Sites. For example, wards can belong to clinics or departments, which can in turn belong to hospitals, which in turn can belong to hospital systems, which in turn can belong to HMOs.The relationships between Care Sites are defined in the FACT_RELATIONSHIP table."
|
||||
PROVIDER,CDM,No,,No,,,"The PROVIDER table contains a list of uniquely identified healthcare providers. These are individuals providing hands-on healthcare to patients, such as physicians, nurses, midwives, physical therapists etc.","Many sources do not make a distinction between individual and institutional providers. The PROVIDER table contains the individual providers. If the source, instead of uniquely identifying individual providers, only provides limited information such as specialty, generic or 'pooled' Provider records are listed in the PROVIDER table.",
|
||||
PAYER_PLAN_PERIOD,CDM,No,,Yes,0,,"The PAYER_PLAN_PERIOD table captures details of the period of time that a Person is continuously enrolled under a specific health Plan benefit structure from a given Payer. Each Person receiving healthcare is typically covered by a health benefit plan, which pays for (fully or partially), or directly provides, the care. These benefit plans are provided by payers, such as health insurances or state or government agencies. In each plan the details of the health benefits are defined for the Person or her family, and the health benefit Plan might change over time typically with increasing utilization (reaching certain cost thresholds such as deductibles), plan availability and purchasing choices of the Person. The unique combinations of Payer organizations, health benefit Plans and time periods in which they are valid for a Person are recorded in this table.","A Person can have multiple, overlapping, Payer_Plan_Periods in this table. For example, medical and drug coverage in the US can be represented by two Payer_Plan_Periods. The details of the benefit structure of the Plan is rarely known, the idea is just to identify that the Plans are different.",
|
||||
- Person, 2, Person, 1, child of"
|
||||
LOCATION,CDM,No,,No,,,The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites.,,"Each address or Location is unique and is present only once in the table. Locations do not contain names, such as the name of a hospital. In order to construct a full address that can be used in the postal service, the address information from the Location needs to be combined with information from the Care Site."
|
||||
CARE_SITE,CDM,No,,No,,,"The CARE_SITE table contains a list of uniquely identified institutional (physical or organizational) units where healthcare delivery is practiced (offices, wards, hospitals, clinics, etc.).",,"Care site is a unique combination of location_id and place_of_service_source_value. Care site does not take into account the provider (human) information such a specialty. Many source data do not make a distinction between individual and institutional providers. The CARE_SITE table contains the institutional providers. If the source, instead of uniquely identifying individual Care Sites, only provides limited information such as Place of Service, generic or ""pooled"" Care Site records are listed in the CARE_SITE table. There can be hierarchical and business relationships between Care Sites. For example, wards can belong to clinics or departments, which can in turn belong to hospitals, which in turn can belong to hospital systems, which in turn can belong to HMOs.The relationships between Care Sites are defined in the FACT_RELATIONSHIP table."
|
||||
PROVIDER,CDM,No,,No,,,"The PROVIDER table contains a list of uniquely identified healthcare providers. These are individuals providing hands-on healthcare to patients, such as physicians, nurses, midwives, physical therapists etc.","Many sources do not make a distinction between individual and institutional providers. The PROVIDER table contains the individual providers. If the source, instead of uniquely identifying individual providers, only provides limited information such as specialty, generic or 'pooled' Provider records are listed in the PROVIDER table.",
|
||||
PAYER_PLAN_PERIOD,CDM,No,,Yes,0,,"The PAYER_PLAN_PERIOD table captures details of the period of time that a Person is continuously enrolled under a specific health Plan benefit structure from a given Payer. Each Person receiving healthcare is typically covered by a health benefit plan, which pays for (fully or partially), or directly provides, the care. These benefit plans are provided by payers, such as health insurances or state or government agencies. In each plan the details of the health benefits are defined for the Person or her family, and the health benefit Plan might change over time typically with increasing utilization (reaching certain cost thresholds such as deductibles), plan availability and purchasing choices of the Person. The unique combinations of Payer organizations, health benefit Plans and time periods in which they are valid for a Person are recorded in this table.","A Person can have multiple, overlapping, Payer_Plan_Periods in this table. For example, medical and drug coverage in the US can be represented by two Payer_Plan_Periods. The details of the benefit structure of the Plan is rarely known, the idea is just to identify that the Plans are different.",
|
||||
COST,CDM,No,,No,,,"The COST table captures records containing the cost of any medical event recorded in one of the OMOP clinical event tables such as DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE, VISIT_DETAIL, DEVICE_OCCURRENCE, OBSERVATION or MEASUREMENT.
|
||||
|
||||
Each record in the cost table account for the amount of money transacted for the clinical event. So, the COST table may be used to represent both receivables (charges) and payments (paid), each transaction type represented by its COST_CONCEPT_ID. The COST_TYPE_CONCEPT_ID field will use concepts in the Standardized Vocabularies to designate the source (provenance) of the cost data. A reference to the health plan information in the PAYER_PLAN_PERIOD table is stored in the record for information used for the adjudication system to determine the persons benefit for the clinical event.","When dealing with summary costs, the cost of the goods or services the provider provides is often not known directly, but derived from the hospital charges multiplied by an average cost-to-charge ratio.","One cost record is generated for each response by a payer. In a claims databases, the payment and payment terms reported by the payer for the goods or services billed will generate one cost record. If the source data has payment information for more than one payer (i.e. primary insurance and secondary insurance payment for one entity), then a cost record is created for each reporting payer. Therefore, it is possible for one procedure to have multiple cost records for each payer, but typically it contains one or no record per entity. Payer reimbursement cost records will be identified by using the PAYER_PLAN_ID field. Drug costs are composed of ingredient cost (the amount charged by the wholesale distributor or manufacturer), the dispensing fee (the amount charged by the pharmacy and the sales tax)."
|
||||
DRUG_ERA,CDM,No,,Yes,0,,"A Drug Era is defined as a span of time when the Person is assumed to be exposed to a particular active ingredient. A Drug Era is not the same as a Drug Exposure: Exposures are individual records corresponding to the source when Drug was delivered to the Person, while successive periods of Drug Exposures are combined under certain rules to produce continuous Drug Eras.",,The SQL script for generating DRUG_ERA records can be found [here](https://ohdsi.github.io/CommonDataModel/sqlScripts.html#drug_eras).
|
||||
DOSE_ERA,CDM,No,,Yes,0,,A Dose Era is defined as a span of time when the Person is assumed to be exposed to a constant dose of a specific active ingredient.,,"Dose Eras will be derived from records in the DRUG_EXPOSURE table and the Dose information from the DRUG_STRENGTH table using a standardized algorithm. Dose Form information is not taken into account. So, if the patient changes between different formulations, or different manufacturers with the same formulation, the Dose Era is still spanning the entire time of exposure to the Ingredient. "
|
||||
Each record in the cost table account for the amount of money transacted for the clinical event. So, the COST table may be used to represent both receivables (charges) and payments (paid), each transaction type represented by its COST_CONCEPT_ID. The COST_TYPE_CONCEPT_ID field will use concepts in the Standardized Vocabularies to designate the source (provenance) of the cost data. A reference to the health plan information in the PAYER_PLAN_PERIOD table is stored in the record for information used for the adjudication system to determine the persons benefit for the clinical event.","When dealing with summary costs, the cost of the goods or services the provider provides is often not known directly, but derived from the hospital charges multiplied by an average cost-to-charge ratio.","One cost record is generated for each response by a payer. In a claims databases, the payment and payment terms reported by the payer for the goods or services billed will generate one cost record. If the source data has payment information for more than one payer (i.e. primary insurance and secondary insurance payment for one entity), then a cost record is created for each reporting payer. Therefore, it is possible for one procedure to have multiple cost records for each payer, but typically it contains one or no record per entity. Payer reimbursement cost records will be identified by using the PAYER_PLAN_ID field. Drug costs are composed of ingredient cost (the amount charged by the wholesale distributor or manufacturer), the dispensing fee (the amount charged by the pharmacy and the sales tax)."
|
||||
DRUG_ERA,CDM,No,,Yes,0,,"A Drug Era is defined as a span of time when the Person is assumed to be exposed to a particular active ingredient. A Drug Era is not the same as a Drug Exposure: Exposures are individual records corresponding to the source when Drug was delivered to the Person, while successive periods of Drug Exposures are combined under certain rules to produce continuous Drug Eras.",,The SQL script for generating DRUG_ERA records can be found [here](https://ohdsi.github.io/CommonDataModel/sqlScripts.html#drug_eras).
|
||||
DOSE_ERA,CDM,No,,Yes,0,,A Dose Era is defined as a span of time when the Person is assumed to be exposed to a constant dose of a specific active ingredient.,,"Dose Eras will be derived from records in the DRUG_EXPOSURE table and the Dose information from the DRUG_STRENGTH table using a standardized algorithm. Dose Form information is not taken into account. So, if the patient changes between different formulations, or different manufacturers with the same formulation, the Dose Era is still spanning the entire time of exposure to the Ingredient. "
|
||||
CONDITION_ERA,CDM,No,,Yes,0,,"A Condition Era is defined as a span of time when the Person is assumed to have a given condition. Similar to Drug Eras, Condition Eras are chronological periods of Condition Occurrence. Combining individual Condition Occurrences into a single Condition Era serves two purposes:
|
||||
|
||||
- It allows aggregation of chronic conditions that require frequent ongoing care, instead of treating each Condition Occurrence as an independent event.
|
||||
|
|
@ -56,26 +56,26 @@ CONDITION_ERA,CDM,No,,Yes,0,,"A Condition Era is defined as a span of time when
|
|||
For example, consider a Person who visits her Primary Care Physician (PCP) and who is referred to a specialist. At a later time, the Person visits the specialist, who confirms the PCP's original diagnosis and provides the appropriate treatment to resolve the condition. These two independent doctor visits should be aggregated into one Condition Era.",,"Each Condition Era corresponds to one or many Condition Occurrence records that form a continuous interval.
|
||||
The condition_concept_id field contains Concepts that are identical to those of the CONDITION_OCCURRENCE table records that make up the Condition Era. In contrast to Drug Eras, Condition Eras are not aggregated to contain Conditions of different hierarchical layers. The SQl Script for generating CONDITION_ERA records can be found [here](https://ohdsi.github.io/CommonDataModel/sqlScripts.html#condition_eras)
|
||||
The Condition Era Start Date is the start date of the first Condition Occurrence.
|
||||
The Condition Era End Date is the end date of the last Condition Occurrence. Condition Eras are built with a Persistence Window of 30 days, meaning, if no occurrence of the same condition_concept_id happens within 30 days of any one occurrence, it will be considered the condition_era_end_date."
|
||||
METADATA,CDM,No,,No,,,The METADATA table contains metadata information about a dataset that has been transformed to the OMOP Common Data Model.,,
|
||||
CDM_SOURCE,CDM,No,,No,,,The CDM_SOURCE table contains detail about the source database and the process used to transform the data into the OMOP Common Data Model.,,
|
||||
The Condition Era End Date is the end date of the last Condition Occurrence. Condition Eras are built with a Persistence Window of 30 days, meaning, if no occurrence of the same condition_concept_id happens within 30 days of any one occurrence, it will be considered the condition_era_end_date."
|
||||
METADATA,CDM,No,,No,,,The METADATA table contains metadata information about a dataset that has been transformed to the OMOP Common Data Model.,,
|
||||
CDM_SOURCE,CDM,No,,No,,,The CDM_SOURCE table contains detail about the source database and the process used to transform the data into the OMOP Common Data Model.,,
|
||||
CONCEPT,VOCAB,No,,No,,,"The Standardized Vocabularies contains records, or Concepts, that uniquely identify each fundamental unit of meaning used to express clinical information in all domain tables of the CDM. Concepts are derived from vocabularies, which represent clinical information across a domain (e.g. conditions, drugs, procedures) through the use of codes and associated descriptions. Some Concepts are designated Standard Concepts, meaning these Concepts can be used as normative expressions of a clinical entity within the OMOP Common Data Model and within standardized analytics. Each Standard Concept belongs to one domain, which defines the location where the Concept would be expected to occur within data tables of the CDM.
|
||||
|
||||
Concepts can represent broad categories (like 'Cardiovascular disease'), detailed clinical elements ('Myocardial infarction of the anterolateral wall') or modifying characteristics and attributes that define Concepts at various levels of detail (severity of a disease, associated morphology, etc.).
|
||||
|
||||
Records in the Standardized Vocabularies tables are derived from national or international vocabularies such as SNOMED-CT, RxNorm, and LOINC, or custom Concepts defined to cover various aspects of observational data analysis. ",,
|
||||
VOCABULARY,VOCAB,No,,No,,,The VOCABULARY table includes a list of the Vocabularies collected from various sources or created de novo by the OMOP community. This reference table is populated with a single record for each Vocabulary source and includes a descriptive name and other associated attributes for the Vocabulary.,,
|
||||
DOMAIN,VOCAB,No,,No,,,"The DOMAIN table includes a list of OMOP-defined Domains the Concepts of the Standardized Vocabularies can belong to. A Domain defines the set of allowable Concepts for the standardized fields in the CDM tables. For example, the ""Condition"" Domain contains Concepts that describe a condition of a patient, and these Concepts can only be stored in the condition_concept_id field of the CONDITION_OCCURRENCE and CONDITION_ERA tables. This reference table is populated with a single record for each Domain and includes a descriptive name for the Domain.",,
|
||||
CONCEPT_CLASS,VOCAB,No,,No,,,"The CONCEPT_CLASS table is a reference table, which includes a list of the classifications used to differentiate Concepts within a given Vocabulary. This reference table is populated with a single record for each Concept Class.",,
|
||||
CONCEPT_RELATIONSHIP,VOCAB,No,,No,,,The CONCEPT_RELATIONSHIP table contains records that define direct relationships between any two Concepts and the nature or type of the relationship. Each type of a relationship is defined in the RELATIONSHIP table.,,
|
||||
RELATIONSHIP,VOCAB,No,,No,,,The RELATIONSHIP table provides a reference list of all types of relationships that can be used to associate any two concepts in the CONCEPT_RELATIONSHP table.,,
|
||||
CONCEPT_SYNONYM,VOCAB,No,,No,,,The CONCEPT_SYNONYM table is used to store alternate names and descriptions for Concepts.,,
|
||||
Records in the Standardized Vocabularies tables are derived from national or international vocabularies such as SNOMED-CT, RxNorm, and LOINC, or custom Concepts defined to cover various aspects of observational data analysis. ",,
|
||||
VOCABULARY,VOCAB,No,,No,,,The VOCABULARY table includes a list of the Vocabularies collected from various sources or created de novo by the OMOP community. This reference table is populated with a single record for each Vocabulary source and includes a descriptive name and other associated attributes for the Vocabulary.,,
|
||||
DOMAIN,VOCAB,No,,No,,,"The DOMAIN table includes a list of OMOP-defined Domains the Concepts of the Standardized Vocabularies can belong to. A Domain defines the set of allowable Concepts for the standardized fields in the CDM tables. For example, the ""Condition"" Domain contains Concepts that describe a condition of a patient, and these Concepts can only be stored in the condition_concept_id field of the CONDITION_OCCURRENCE and CONDITION_ERA tables. This reference table is populated with a single record for each Domain and includes a descriptive name for the Domain.",,
|
||||
CONCEPT_CLASS,VOCAB,No,,No,,,"The CONCEPT_CLASS table is a reference table, which includes a list of the classifications used to differentiate Concepts within a given Vocabulary. This reference table is populated with a single record for each Concept Class.",,
|
||||
CONCEPT_RELATIONSHIP,VOCAB,No,,No,,,The CONCEPT_RELATIONSHIP table contains records that define direct relationships between any two Concepts and the nature or type of the relationship. Each type of a relationship is defined in the RELATIONSHIP table.,,
|
||||
RELATIONSHIP,VOCAB,No,,No,,,The RELATIONSHIP table provides a reference list of all types of relationships that can be used to associate any two concepts in the CONCEPT_RELATIONSHP table.,,
|
||||
CONCEPT_SYNONYM,VOCAB,No,,No,,,The CONCEPT_SYNONYM table is used to store alternate names and descriptions for Concepts.,,
|
||||
CONCEPT_ANCESTOR,VOCAB,No,,No,,,"The CONCEPT_ANCESTOR table is designed to simplify observational analysis by providing the complete hierarchical relationships between Concepts. Only direct parent-child relationships between Concepts are stored in the CONCEPT_RELATIONSHIP table. To determine higher level ancestry connections, all individual direct relationships would have to be navigated at analysis time. The CONCEPT_ANCESTOR table includes records for all parent-child relationships, as well as grandparent-grandchild relationships and those of any other level of lineage. Using the CONCEPT_ANCESTOR table allows for querying for all descendants of a hierarchical concept. For example, drug ingredients and drug products are all descendants of a drug class ancestor.
|
||||
|
||||
This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP and RELATIONSHIP tables.",,
|
||||
SOURCE_TO_CONCEPT_MAP,VOCAB,No,,No,,,"The source to concept map table is a legacy data structure within the OMOP Common Data Model, recommended for use in ETL processes to maintain local source codes which are not available as Concepts in the Standardized Vocabularies, and to establish mappings for each source code into a Standard Concept as target_concept_ids that can be used to populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table is no longer populated with content within the Standardized Vocabularies published to the OMOP community.",,
|
||||
DRUG_STRENGTH,VOCAB,No,,No,,,The DRUG_STRENGTH table contains structured content about the amount or concentration and associated units of a specific ingredient contained within a particular drug product. This table is supplemental information to support standardized analysis of drug utilization.,,
|
||||
COHORT_DEFINITION,VOCAB,No,,No,,,"The COHORT_DEFINITION table contains records defining a Cohort derived from the data through the associated description and syntax and upon instantiation (execution of the algorithm) placed into the COHORT table. Cohorts are a set of subjects that satisfy a given combination of inclusion criteria for a duration of time. The COHORT_DEFINITION table provides a standardized structure for maintaining the rules governing the inclusion of a subject into a cohort, and can store operational programming code to instantiate the cohort within the OMOP Common Data Model.",,
|
||||
This table is entirely derived from the CONCEPT, CONCEPT_RELATIONSHIP and RELATIONSHIP tables.",,
|
||||
SOURCE_TO_CONCEPT_MAP,VOCAB,No,,No,,,"The source to concept map table is a legacy data structure within the OMOP Common Data Model, recommended for use in ETL processes to maintain local source codes which are not available as Concepts in the Standardized Vocabularies, and to establish mappings for each source code into a Standard Concept as target_concept_ids that can be used to populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table is no longer populated with content within the Standardized Vocabularies published to the OMOP community.",,
|
||||
DRUG_STRENGTH,VOCAB,No,,No,,,The DRUG_STRENGTH table contains structured content about the amount or concentration and associated units of a specific ingredient contained within a particular drug product. This table is supplemental information to support standardized analysis of drug utilization.,,
|
||||
COHORT_DEFINITION,VOCAB,No,,No,,,"The COHORT_DEFINITION table contains records defining a Cohort derived from the data through the associated description and syntax and upon instantiation (execution of the algorithm) placed into the COHORT table. Cohorts are a set of subjects that satisfy a given combination of inclusion criteria for a duration of time. The COHORT_DEFINITION table provides a standardized structure for maintaining the rules governing the inclusion of a subject into a cohort, and can store operational programming code to instantiate the cohort within the OMOP Common Data Model.",,
|
||||
ATTRIBUTE_DEFINITION,VOCAB,No,,No,,,"The ATTRIBUTE_DEFINITION table contains records to define each attribute
|
||||
through an associated description and syntax. Attributes are derived elements
|
||||
that can be selected or calculated for a subject within a cohort. The
|
||||
|
|
|
|||
|
|
|
@ -19,7 +19,7 @@ The Visit duration, or 'length of stay', is defined as VISIT_END_DATE - VISIT_ST
|
|||
VISIT_DETAIL,CDM,No,VISIT_DETAIL_,Yes,0,,The VISIT_DETAIL table is an optional table used to represents details of each record in the parent VISIT_OCCURRENCE table. A good example of this would be the movement between units in a hospital during an inpatient stay or claim lines associated with a one insurance claim. For every record in the VISIT_OCCURRENCE table there may be 0 or more records in the VISIT_DETAIL table with a 1:n relationship where n may be 0. The VISIT_DETAIL table is structurally very similar to VISIT_OCCURRENCE table and belongs to the visit domain.,"The configuration defining the Visit Detail is described by Concepts in the Visit Domain, which form a hierarchical structure. The Visit Detail record will have an associated to the Visit Occurrence record in two ways: <br> 1. The Visit Detail record will have the VISIT_OCCURRENCE_ID it is associated to 2. The VISIT_DETAIL_CONCEPT_ID will be a descendant of the VISIT_CONCEPT_ID for the Visit.","It is not mandatory that the VISIT_DETAIL table be filled in, but if you find that the logic to create VISIT_OCCURRENCE records includes the roll-up of multiple smaller records to create one picture of a Visit then it is a good idea to use VISIT_DETAIL. In EHR data, for example, a Person may be in the hospital but instead of one over-arching Visit their encounters are recorded as times they interacted with a health care provider. A Person in the hospital interacts with multiple providers multiple times a day so the encounters must be strung together using some heuristic (defined by the ETL) to identify the entire Visit. In this case the encounters would be considered Visit Details and the entire Visit would be the Visit Occurrence. In this example it is also possible to use the Vocabulary to distinguish Visit Details from a Visit Occurrence by setting the VISIT_CONCEPT_ID to [9201](https://athena.ohdsi.org/search-terms/terms/9201) and the VISIT_DETAIL_CONCEPT_IDs either to 9201 or its children to indicate where the patient was in the hospital at the time of care."
|
||||
CONDITION_OCCURRENCE,CDM,No,CONDITION_,Yes,0,,"This table contains records of Events of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign, or a symptom, which is either observed by a Provider or reported by the patient. ","Conditions are defined by Concepts from the Condition domain, which form a complex hierarchy. As a result, the same Person with the same disease may have multiple Condition records, which belong to the same hierarchical family. Most Condition records are mapped from diagnostic codes, but recorded signs, symptoms and summary descriptions also contribute to this table. Rule out diagnoses should not be recorded in this table, but in reality their negating nature is not always captured in the source data, and other precautions must be taken when when identifying Persons who should suffer from the recorded Condition. Record all conditions as they exist in the source data. Any decisions about diagnosis/phenotype definitions would be done through cohort specifications. These cohorts can be housed in the [COHORT](https://ohdsi.github.io/CommonDataModel/cdm531.html#payer_plan_period) table. Conditions span a time interval from start to end, but are typically recorded as single snapshot records with no end date. The reason is twofold: (i) At the time of the recording the duration is not known and later not recorded, and (ii) the Persons typically cease interacting with the healthcare system when they feel better, which leads to incomplete capture of resolved Conditions. The [CONDITION_ERA](https://ohdsi.github.io/CommonDataModel/cdm531.html#condition_era) table addresses this issue. Family history and past diagnoses ('history of') are not recorded in this table. Instead, they are listed in the [OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table. Codes written in the process of establishing the diagnosis, such as 'question of' of and 'rule out', should not represented here. Instead, they should be recorded in the [OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table, if they are used for analyses. However, this information is not always available.",Source codes and source text fields mapped to Standard Concepts of the Condition Domain have to be recorded here.
|
||||
DRUG_EXPOSURE,CDM,No,DRUG_,Yes,0,,"This table captures records about the exposure to a Drug ingested or otherwise introduced into the body. A Drug is a biochemical substance formulated in such a way that when administered to a Person it will exert a certain biochemical effect on the metabolism. Drugs include prescription and over-the-counter medicines, vaccines, and large-molecule biologic therapies. Radiological devices ingested or applied locally do not count as Drugs.","The purpose of records in this table is to indicate an exposure to a certain drug as best as possible. In this context a drug is defined as an active ingredient. Drug Exposures are defined by Concepts from the Drug domain, which form a complex hierarchy. As a result, one DRUG_SOURCE_CONCEPT_ID may map to multiple standard concept ids if it is a combination product. Records in this table represent prescriptions written, prescriptions dispensed, and drugs administered by a provider to name a few. The DRUG_TYPE_CONCEPT_ID can be used to find and filter on these types. This table includes additional information about the drug products, the quantity given, and route of administration.",Information about quantity and dose is provided in a variety of different ways and it is important for the ETL to provide as much information as possible from the data. Depending on the provenance of the data fields may be captured differently i.e. quantity for drugs administered may have a separate meaning from quantity for prescriptions dispensed. If a patient has multiple records on the same day for the same drug or procedures the ETL should not de-dupe them unless there is probable reason to believe the item is a true data duplicate. Take note on how to handle refills for prescriptions written.
|
||||
PROCEDURE_OCCURRENCE,CDM,No,PROCEDURE_,Yes,0,,"This table contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient with a diagnostic or therapeutic purpose.","Lab tests are not a procedure, if something is observed with an expected resulting amount and unit then it should be a measurement. Phlebotomy is a procedure but so trivial that it tends to be rarely captured. It can be assumed that there is a phlebotomy procedure associated with many lab tests, therefore it is unnecessary to add them as separate procedures. If the user finds the same procedure over concurrent days, it is assumed those records are part of a procedure lasting more than a day. This logic is in lieu of the procedure_end_date, which will be added in a future version of the CDM.","If a procedure lasts more than a day, then it should be recorded as a separate record for each day the procedure occurred, this logic is in lieu of the PROCEDURE_END_DATE, which will be added in a future version of the CDM. When dealing with duplicate records, the ETL must determine whether to sum them up into one record or keep them separate. Things to consider are: - Same Procedure - Same PROCEDURE_DATETIME - Same Visit Occurrence or Visit Detail - Same Provider - Same Modifier for Procedures. Source codes and source text fields mapped to Standard Concepts of the Procedure Domain have to be recorded here."
|
||||
PROCEDURE_OCCURRENCE,CDM,No,PROCEDURE_,Yes,0,,"This table contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient with a diagnostic or therapeutic purpose.","Lab tests are not a procedure, if something is observed with an expected resulting amount and unit then it should be a measurement. Phlebotomy is a procedure but so trivial that it tends to be rarely captured. It can be assumed that there is a phlebotomy procedure associated with many lab tests, therefore it is unnecessary to add them as separate procedures. If the user finds the same procedure over concurrent days, it is assumed those records are part of a procedure lasting more than a day. This logic is in lieu of the procedure_end_date, which will be added in a future version of the CDM.","When dealing with duplicate records, the ETL must determine whether to sum them up into one record or keep them separate. Things to consider are: - Same Procedure - Same PROCEDURE_DATETIME - Same Visit Occurrence or Visit Detail - Same Provider - Same Modifier for Procedures. Source codes and source text fields mapped to Standard Concepts of the Procedure Domain have to be recorded here."
|
||||
DEVICE_EXPOSURE,CDM,No,DEVICE_,Yes,0,,"The Device domain captures information about a person's exposure to a foreign physical object or instrument which is used for diagnostic or therapeutic purposes through a mechanism beyond chemical action. Devices include implantable objects (e.g. pacemakers, stents, artificial joints), medical equipment and supplies (e.g. bandages, crutches, syringes), other instruments used in medical procedures (e.g. sutures, defibrillators) and material used in clinical care (e.g. adhesives, body material, dental material, surgical material).","The distinction between Devices or supplies and Procedures are sometimes blurry, but the former are physical objects while the latter are actions, often to apply a Device or supply.",Source codes and source text fields mapped to Standard Concepts of the Device Domain have to be recorded here.
|
||||
MEASUREMENT,CDM,No,MEASUREMENT_,Yes,0,,"The MEASUREMENT table contains records of Measurements, i.e. structured values (numerical or categorical) obtained through systematic and standardized examination or testing of a Person or Person's sample. The MEASUREMENT table contains both orders and results of such Measurements as laboratory tests, vital signs, quantitative findings from pathology reports, etc. Measurements are stored as attribute value pairs, with the attribute as the Measurement Concept and the value representing the result. The value can be a Concept (stored in VALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with a Unit (UNIT_CONCEPT_ID). The Procedure for obtaining the sample is housed in the PROCEDURE_OCCURRENCE table, though it is unnecessary to create a PROCEDURE_OCCURRENCE record for each measurement if one does not exist in the source data. Measurements differ from Observations in that they require a standardized test or some other activity to generate a quantitative or qualitative result. If there is no result, it is assumed that the lab test was conducted but the result was not captured.","Measurements are predominately lab tests with a few exceptions, like blood pressure or function tests. Results are given in the form of a value and unit combination. When investigating measurements, look for operator_concept_ids (<, >, etc.).","Only records where the source value maps to a Concept in the measurement domain should be included in this table. Even though each Measurement always has a result, the fields VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are not mandatory as often the result is not given in the source data. When the result is not known, the Measurement record represents just the fact that the corresponding Measurement was carried out, which in itself is already useful information for some use cases. For some Measurement Concepts, the result is included in the test. For example, ICD10 CONCEPT_ID [45548980](https://athena.ohdsi.org/search-terms/terms/45548980) 'Abnormal level of unspecified serum enzyme' indicates a Measurement and the result (abnormal). In those situations, the CONCEPT_RELATIONSHIP table in addition to the 'Maps to' record contains a second record with the relationship_id set to 'Maps to value'. In this example, the 'Maps to' relationship directs to [4046263](https://athena.ohdsi.org/search-terms/terms/4046263) 'Enzyme measurement' as well as a 'Maps to value' record to [4135493](https://athena.ohdsi.org/search-terms/terms/4135493) 'Abnormal'."
|
||||
OBSERVATION,CDM,No,OBSERVATION_,Yes,0,,"The OBSERVATION table captures clinical facts about a Person obtained in the context of examination, questioning or a procedure. Any data that cannot be represented by any other domains, such as social and lifestyle facts, medical history, family history, etc. are recorded here.","Observations differ from Measurements in that they do not require a standardized test or some other activity to generate clinical fact. Typical observations are medical history, family history, the stated need for certain treatment, social circumstances, lifestyle choices, healthcare utilization patterns, etc. If the generation clinical facts requires a standardized testing such as lab testing or imaging and leads to a standardized result, the data item is recorded in the MEASUREMENT table. If the clinical fact observed determines a sign, symptom, diagnosis of a disease or other medical condition, it is recorded in the CONDITION_OCCURRENCE table. Valid Observation Concepts are not enforced to be from any domain though they still should be Standard Concepts.","Records whose Source Values map to any domain besides Condition, Procedure, Drug, Measurement or Device should be stored in the Observation table. Observations can be stored as attribute value pairs, with the attribute as the Observation Concept and the value representing the clinical fact. This fact can be a Concept (stored in VALUE_AS_CONCEPT), a numerical value (VALUE_AS_NUMBER), a verbatim string (VALUE_AS_STRING), or a datetime (VALUE_AS_DATETIME). Even though Observations do not have an explicit result, the clinical fact can be stated separately from the type of Observation in the VALUE_AS_* fields. It is recommended for Observations that are suggestive statements of positive assertion should have a value of 'Yes' (concept_id=4188539), recorded, even though the null value is the equivalent. "
|
||||
|
|
|
|||
|
|
|
@ -1,2 +1,4 @@
|
|||
setwd("/Users/clairblacketer/Documents/Github/CommonDataModel/rmd")#
|
||||
rmarkdown::render_site()
|
||||
setwd("/Users/clairblacketer/Documents/Github/CommonDataModel/rmd")#
|
||||
rmarkdown::render_site()
|
||||
|
|
|
|||
|
|
@ -48,9 +48,11 @@ navbar:
|
|||
href: cdm54.html
|
||||
- text: "Changes from CDM v5.3"
|
||||
href: cdm54Changes.html
|
||||
- text: "Proposals"
|
||||
- text: "CDM Proposals"
|
||||
icon: fa-plus-square
|
||||
menu:
|
||||
- text: "How to Propose Changes to the CDM"
|
||||
href: cdmRequestProcess.html
|
||||
- text: "Under Review"
|
||||
href: https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal
|
||||
- text: "Accepted"
|
||||
|
|
@ -69,6 +71,8 @@ navbar:
|
|||
- text: "Support"
|
||||
icon: fa-life-ring
|
||||
menu:
|
||||
- text: "Help! My Data Doesn't Fit!"
|
||||
href: cdmDecisionTree.html
|
||||
- text: "FAQ"
|
||||
href: faq.html
|
||||
- text: "SQL Scripts"
|
||||
|
|
|
|||
|
|
@ -92,9 +92,9 @@ for(tb in tables) {
|
|||
|
||||
print(kable(x = loopTable, align = "l", row.names = FALSE, format = "html", escape = FALSE) %>%
|
||||
column_spec(1, bold = T) %>%
|
||||
column_spec(2, width = "3in", include_thead = T) %>%
|
||||
column_spec(3, width = "4in", include_thead = T) %>%
|
||||
column_spec(4:9, width = "1in", include_thead = T) %>%
|
||||
# column_spec(2, width = "3in", include_thead = T) %>%
|
||||
# column_spec(3, width = "4in", include_thead = T) %>%
|
||||
# column_spec(4:9, width = "1in", include_thead = T) %>%
|
||||
kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13))
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -108,9 +108,9 @@ for(tb in tables) {
|
|||
|
||||
print(kable(x = loopTable, align = "l", row.names = FALSE, format = "html", escape = FALSE) %>%
|
||||
column_spec(1, bold = T) %>%
|
||||
column_spec(2, width = "3in", include_thead = T) %>%
|
||||
column_spec(3, width = "4in", include_thead = T) %>%
|
||||
column_spec(4:9, width = "1in", include_thead = T) %>%
|
||||
# column_spec(2, width = "3in", include_thead = T) %>%
|
||||
# column_spec(3, width = "4in", include_thead = T) %>%
|
||||
# column_spec(4:9, width = "1in", include_thead = T) %>%
|
||||
kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13))
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -104,9 +104,9 @@ for(tb in tables) {
|
|||
|
||||
print(kable(x = loopTable, align = "l", row.names = FALSE, format = "html") %>%
|
||||
column_spec(1, bold = T) %>%
|
||||
column_spec(2, width = "3in", include_thead = T) %>%
|
||||
column_spec(3, width = "4in", include_thead = T) %>%
|
||||
column_spec(4:9, width = "1in", include_thead = T) %>%
|
||||
# column_spec(2, width = "3in", include_thead = T) %>%
|
||||
# column_spec(3, width = "4in", include_thead = T) %>%
|
||||
# column_spec(4:9, width = "1in", include_thead = T) %>%
|
||||
kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13))
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,13 @@
|
|||
---
|
||||
title: '<div><img src="ohdsi40x40.png"></img> CDM Request Decision Tree </div>'
|
||||
output:
|
||||
html_document
|
||||
---
|
||||
|
||||
If you have arrived to this page then you must be thinking **HELP! I have some data that doesn't fit in the CDM!** Never fear as this handy guide will point you in the right direction and all you have to do is answer a few questions.
|
||||
|
||||
**First things first, do you think you will need to change the OMOP Common Data Model itself or are you solely looking for vocabulary support?**
|
||||
|
||||
[I think I need to change the OMOP CDM](networkUseCase.html)
|
||||
|
||||
[I need vocabulary support](vocabN.html)
|
||||
|
|
@ -8,29 +8,31 @@ output:
|
|||
|
||||
The OMOP Common Data Model is managed by the OHDSI CDM Working Group. The formal remit of the CDM Working Group (WG) is to hear proposals for change, ratifying only those with valid use cases and data to support them. Then, once ratified, these proposals are incorporated into the next version of the CDM. In the past, this was done by the WG alone. The group would invite others from around the community to present use cases for change and suggestions for improvement. The WG would then vote on the proposals and a new CDM version would be released after a certain period of time or if enough proposals were voted in. This approach worked when the community was smaller but as it is growing rapidly the CDM WG needed to adapt the refresh cycle such that everyone has an opportunity to weigh in on the proposed changes.
|
||||
|
||||
Looking to make a change or addition to the OMOP CDM? Please answer the questions in the [decision tree](cdmDecisionTree.html) to point you in the right direction.
|
||||
|
||||
## CDM Refresh Cycle
|
||||
|
||||
|
||||
|
||||
### 1. Define New Version [Completed for v5.4]
|
||||
### 1. Define New Version
|
||||
|
||||
The image above describes the new CDM refresh cycle. It begins with **defining a new version**. This has been completed for the current cycle. Issues and proposals on the github were considered during a 4-hour workshop where it was decided the next CDM version will be CDM v5.4, building off of CDM v5.3. The group then participated in a rapid-fire voting activity to identify which changes should be incorporated into CDM v5.4. Any items that were not unanimously agreed upon were then discussed in small groups to hone the proposal and suggestions were presented back to the group. The final roadmap for CDM v5.4 can be found [here](https://github.com/OHDSI/CommonDataModel/projects/3).
|
||||
The image above describes the new CDM refresh cycle. It begins with **defining a new version**. Proposals are heard over the course of a year according to the [CDM Request Process](cdmRequestProcess.html) and the ratified changes are added to the roadmap until such time that there are enough updates to warrant a new version of the model.
|
||||
|
||||
Looking to open a proposal to change or augment the CDM? Please open an [issue](https://github.com/OHDSI/CommonDataModel/issues) and use the **proposal template**.
|
||||
Looking to open a proposal to change or augment the CDM? Please follow the questions in the [decision tree](cdmDecisionTree.html) to help you determine what you will need.
|
||||
|
||||
### 2. Sign off from Work Groups [Completed for v5.4]
|
||||
### 2. Sign off from Work Groups
|
||||
|
||||
Each member of the CDM WG is a liaison for another workgroup in the community. They are responsible for presenting the proposed changes to the CDM and collecting the feedback. This has resulted in very helpful suggestions from the EHR, Data Quality, Device, HADES, and ACHILLES groups. This outreach has proven to be very effective and should result in a very stable version.
|
||||
|
||||
### 3. Release DDLs
|
||||
### 3. Release DDLs
|
||||
|
||||
After all changes and suggestions are agreed upon by the community and work groups the next step is to generate the DDLs. The CDM WG hosted a hackathon on August 18-19, 2021. During this time the group created an R package to automatically generate the DDLs and the code to instantiate an empty CDM instance. Changes were made to v5.3 to generate v5.4 and the repository was refactored.
|
||||
After all changes and suggestions are agreed upon by the community and work groups the next step is to generate the DDLs. For example, the CDM WG hosted a hackathon on August 18-19, 2021. During this time the group created an R package to automatically generate the DDLs and the code to instantiate an empty CDM instance. Changes were made to v5.3 to generate v5.4 and the repository was refactored.
|
||||
|
||||
### 4. Software Update
|
||||
### 4. Software Update
|
||||
|
||||
There will be period of time once the DDLs are ready to allow the software and methods developers to prepare for the official release of the CDM. This is meant to serve as a buffer so that once the community starts adopting the new model, the tools and methods will be ready to support it.
|
||||
|
||||
### 5. Community Support
|
||||
### 5. Community Support
|
||||
|
||||
This is the final stage of the CDM refresh cycle. Once the DDLs are ready and the software and tools supports the new version, the CDM WG will work to help the community convert their data to the new model.
|
||||
|
||||
|
|
@ -39,7 +41,7 @@ This is the final stage of the CDM refresh cycle. Once the DDLs are ready and th
|
|||
|
||||
The CDM working group meets the first and third Tuesday of the month. See below for links to the meetings.
|
||||
|
||||
**Every first Tuesday of the month at 1pm est** [Teams Meeting](https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d)
|
||||
**Every first Tuesday of the month at 10am est** [Teams Meeting](https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d)
|
||||
|
||||
**Every third Tuesday of the month at 1pm est** [Teams Meeting](https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1611000164347?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%223c193b7f-c2ab-4bcf-b88c-f89a6b1fba38%22%7d)
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,91 @@
|
|||
---
|
||||
title: '<div><img src="ohdsi40x40.png"></img> How to Request Changes to the CDM </div>'
|
||||
output:
|
||||
html_document:
|
||||
toc: TRUE
|
||||
toc_float: TRUE
|
||||
---
|
||||
|
||||
Are you in the right place? Please answer the questions in the [decision tree](cdmDecisionTree.html) prior to beginning a CDM Request to make sure you aren't missing something.
|
||||
|
||||
As OHDSI is an open-source community working towards developing a Common Data Model that fulfills the needs of its users, it is often the case that changes need to be made to the model as the community and its research continues to mature. However, the number of people, institutions, and initiatives that rely on the OMOP CDM to advance the science of observational health has grown dramatically since its inception in 2015. Therefore, care must be taken when considering any update to the model, big or small. This document outlines the process that should be taken to ratify a change to the CDM.
|
||||
|
||||
**If you would like guidance prior to starting this process, consider contacting us on our [GitHub](https://github.com/OHDSI/CommonDataModel) or [Teams Channel](https://teams.microsoft.com/l/team/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/conversations?groupId=a6f2c516-e568-4974-8f1e-a7bdc2f997c5&tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5).**
|
||||
|
||||
|
||||
### Scope
|
||||
|
||||
- What kind of changes?
|
||||
- Minor, e.g. new field in existing table
|
||||
- Major, e.g. breaking changes, additional tables
|
||||
- Who can propose changes?
|
||||
- Individuals, OHDSI working groups, organizations
|
||||
|
||||
## Step 1: Proposal
|
||||
|
||||
Once a group or organization has decided on the update they would like made to the model, they must produce a document including the following:
|
||||
|
||||
1. A clear description of the change or addition including the User Guide and ETL Conventions in the same structure as what is present on the website for every table and field currently in the CDM.
|
||||
2. A clearly defined use case noting why the latest version of the OMOP CDM fails to adequately address said use case. This should include describing what you have already tried with the latest version of the OMOP CDM and why it does not meet your needs.
|
||||
3. An example of how the requested change or addition will be used in practice. This can be in the form of sample data, SQL code, a diagram, or text. The proposal can optionally include suggestions as to how other OHDSI tools (Achilles, DataQualityDashboard, Atlas, etc.) should work with your change or addition.
|
||||
|
||||
Once the document is ready to submit, please email [CDM Proposals - Workgroup - Common Data Model](mailto:a58abde7.ohdsi.org@amer.teams.ms). This will go directly to a separate channel in the OHDSI Teams environment that is available to all members of the CDM Working Group.
|
||||
After submitting your document with your proposal to email listed above, someone in the OMOP CDM Working Group will respond to you within 2 weeks. The potential outcomes are as follows:
|
||||
|
||||
- Proposal merits further review (move on to next steps)
|
||||
- Proposal is not ready for workgroup review due to one or more factors
|
||||
- Incomplete
|
||||
- Insufficiently aligned with the OMOP framework
|
||||
- Poorly described use case
|
||||
|
||||
## Step 2: Initial Presentation
|
||||
|
||||
Should your proposals merit further review, the OMOP CDM Working Group will reach out to you to schedule a time for you to present your case at an upcoming meeting. You will be given 15-30 minutes to present your document and you can include anything you feel will help illustrate the need and your potential solution. The group will then discuss, ask questions, and potentially offer other solutions. Depending on the nature of the request, this may go over multiple sessions and you may be asked to make changes to your initial design. At the end of this process your proposal will then be put to consensus in the CDM WG. If the group decides no, they will give feedback describing why they did not feel your proposal should be accepted at this time. If the group decides yes, you move on to step 3.
|
||||
|
||||
**Potential Decision Criteria:**
|
||||
|
||||
- If the change is foundational to OHDSI tools, then the proposal will be put to the larger community open to public comment
|
||||
- How generalizable is your change? Can it be readily applied to other use cases?
|
||||
- Are the proposed changes/additions well designed from a modeling perspective? Do they follow the existing OMOP CDM conventions?
|
||||
- What are the consequences of the change? Are they potentially breaking changes or are they just changes to existing conventions? Will they require the remapping of existing OMOP datasources?
|
||||
- How complicated is your change? Is it an addition of a field or multiple tables?
|
||||
|
||||
## Step 3: Preliminary Decision
|
||||
|
||||
If the proposal is accepted in the preliminary decision, then a branch will be created in the CommonDataModel repository, based on the latest version of the OMOP CDM in use (currently v5.4). It will then be your responsibility to apply the change programmatically in this branch. This should include:
|
||||
|
||||
- Updating the CSV file with the CDM specification, including the User Guide and ETL Conventions documentation
|
||||
- Generating the DDL files with the change
|
||||
- Testing the new DDL files in at least one supported environment
|
||||
|
||||
Once the DDLs with the proposed change are created and tested, you should then ETL some data (either real or synthetic) into the new table/fields. Then, an example cohort should be created that utilizes the change or addition and clearly displays how it can be used in a real study. It is expected that during this stage the proposal will change as you work through your idea in a tangible environment.
|
||||
|
||||
**Potential Decision Criteria:**
|
||||
|
||||
- How would you evaluate the quality of this new field/table?
|
||||
- What characterizations would you perform?
|
||||
- How would you perform a study using this new feature?
|
||||
|
||||
**Potential Outcomes:**
|
||||
|
||||
- Proposal demonstrates merit for further consideration as:
|
||||
- a core data model change (move on to next steps)
|
||||
- an extension (how do we deal with these/do we have ownership of them?)
|
||||
- Proposal does not demonstrate merit for further consideration at this time, and:
|
||||
- recommend as a LOCAL extension
|
||||
- recommend a different course
|
||||
|
||||
## Step 4: Final Presentation
|
||||
|
||||
After generating, testing, and implementing your proposal in a real-world environment the CDM working group will invite you again to present your findings in another 15-30 minute presentation. This should include learnings from the exercise and any updates made to the initial proposal.
|
||||
|
||||
## Step 5: Final Decision
|
||||
|
||||
At this point, the working group liaisons will also take the proposal to other groups to elicit feedback. Then the CDM working group will vote and give a final decision on the proposed change. If ratified, the branch in the repository will be merged into the develop branch to be included in a next version of the OMOP Common Data Model.
|
||||
|
||||
The change should initiate requests for features in tools. The end of this process should be a trigger for using the new feature as per the use case. The group should also produce at least one query for the query library on how to work with the new addition/change.
|
||||
|
||||
### Resources
|
||||
|
||||
“Implementing & adopting a customized OMOP Common Data Model” (Melany Philofsky, OHDSI Symposium 2021) https://www.ohdsi.org/2021-global-symposium-showcase-18/
|
||||
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
---
|
||||
title: "Contact the Vocab Team"
|
||||
output: html_document
|
||||
---
|
||||
|
||||
Okay so you have something you would like to add to the CDM but there is not an existing OMOP vocabulary nor an open-source vocabulary we can bring in to support it. **In this case, please contact the vocabulary team on next steps** as data elements in the CDM must have a vocabulary in place before they can be implemented.
|
||||
|
||||
[Vocabulary Teams Channel](https://teams.microsoft.com/l/channel/19%3a31208179438d45749ff484124e7b1e5e%40thread.tacv2/Vocabulary%2520Subgroup?groupId=a6f2c516-e568-4974-8f1e-a7bdc2f997c5&tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5)
|
||||
|
||||
Once you come to consensus with the vocabulary team regarding your needs, please follow the [CDM Request Process](cdmRequestProcess.html) to begin the steps soliciting a change or addition to the model itself. Need more guidance? Consider contacting the CDM Working Group on our [GitHub](https://github.com/OHDSI/CommonDataModel) or [Teams Channel](https://teams.microsoft.com/l/team/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/conversations?groupId=a6f2c516-e568-4974-8f1e-a7bdc2f997c5&tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5).
|
||||
28
rmd/faq.Rmd
28
rmd/faq.Rmd
|
|
@ -1,11 +1,12 @@
|
|||
---
|
||||
title: "OMOP CDM Frequently Asked Questions"
|
||||
output:
|
||||
html_document
|
||||
|
||||
html_document:
|
||||
toc: yes
|
||||
toc_depth: 5
|
||||
toc_float: yes
|
||||
---
|
||||
|
||||
|
||||
**1. I understand that the common data model (CDM) is a way of organizing disparate data sources into the same relational database design, but how can it be effective since many databases use different coding schemes?**
|
||||
|
||||
During the extract, transform, load (ETL) process of converting a data source into the OMOP common data model, we standardize the structure (e.g. tables, fields, data types), conventions (e.g. rules that govern how source data should be represented), and content (e.g. what common vocabularies are used to speak the same language across clinical domains). The common data model preserves all source data, including the original source vocabulary codes, but adds the standardized vocabularies to allow for network research across the entire OHDSI research community.
|
||||
|
|
@ -171,3 +172,24 @@ Queries are written in R and SQL. The [SqlRender](https://github.com/OHDSI/sqlre
|
|||
OHDSI runs as a distributed data network. All analyses are publicly available and can be downloaded to run at each site. The packages can be run locally and, at the data partner’s discretion, aggregate results can be shared with the study coordinator.
|
||||
|
||||
Data partners can also make use of one of OHDSI's open-source tools called [ARACHNE](https://github.com/OHDSI/arachne), a tool to facilitate distributed network analytics against the OMOP CDM.
|
||||
|
||||
## Recommended System Requirements
|
||||
|
||||
It is difficult to recommend what technical capabilities a site needs to set up an ETL because it is heavily dependent on the amount of data they have and how they plan to use it. Here are some examples of options that have worked well for small to medium organizations and large organizations:
|
||||
|
||||
**Small-to-Medium Organization**
|
||||
|
||||
- CDM size is 100MB to several GBs
|
||||
- Vocab ~20GB
|
||||
- Results < 500 MB
|
||||
- Recommend
|
||||
- Server class machine disk >= 250GB (SSD preferred), >= 4 cores, >= 32GB RAM
|
||||
|
||||
**Large Organization**
|
||||
|
||||
- CDM size is 12GB to several TBs
|
||||
- Vocab ~20GB
|
||||
- Results < 500 MB
|
||||
- Recommend
|
||||
- Cloud-based infrastructure like multiple AWS Redshift clusters, for example:
|
||||
- 
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 38 KiB |
|
|
@ -46,13 +46,12 @@ The CDM is managed by the OHDSI CDM Working Group. If you would like to join our
|
|||
|
||||
The CDM working group meets the first and third Tuesday of the month. See below for links to the meetings.
|
||||
|
||||
**Every first Tuesday of the month at 1pm est** [Teams Meeting](https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d)
|
||||
**Every first Tuesday of the month at 10am est** [Teams Meeting](https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d)
|
||||
|
||||
**Every third Tuesday of the month at 1pm est** [Teams Meeting](https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1611000164347?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%223c193b7f-c2ab-4bcf-b88c-f89a6b1fba38%22%7d)
|
||||
|
||||
|
||||
**Note** If you do you have access to the OHDSI Teams Tenet, either contact Clair Blacketer at mblacke@its.jnj.com or fill out [this form]
|
||||
(https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu) and check "Common Data Model"
|
||||
**Note** If you do you have access to the OHDSI Teams Tenet, either contact Clair Blacketer at mblacke@its.jnj.com or fill out [this form](https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu) and check "Common Data Model"
|
||||
|
||||
### CDM WG Important Links
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,6 @@
|
|||
---
|
||||
title: "Leave As Is"
|
||||
output: html_document
|
||||
---
|
||||
|
||||
Okay, so you do not have a network use case but multiple collaborators have access to the element you are interested in adding to the CDM. **In this circumstance, the CDM Working Group suggests leaving the model as-is.** Without a network use case there is no need to augment the data model. If this is something you need for your work, consider a [local change](localChange.html) or a model extension.
|
||||
|
|
@ -0,0 +1,6 @@
|
|||
---
|
||||
title: "Local Change"
|
||||
output: html_document
|
||||
---
|
||||
|
||||
Since you do not have a network use case and this element is specific to your data source, **feel free to create a local change to your instance of the OMOP Common Data Model.** Augmenting the model at your institution for administrative purposes or other in-house needs is totally acceptable with the understanding that any local changes cannot and should not be relied upon in network studies or supported by the open-source tools.
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
---
|
||||
title: "Network Use Case"
|
||||
output: html_document
|
||||
---
|
||||
|
||||
Alright, so you think you might need to change the OMOP Common Data Model. **Do you have a documented network use case for this data need? This could take the form of an upcoming study or a convention for how to store information.** In this scenario, at least two or more collaborators with data to contribute constitute a network need.
|
||||
|
||||
[Yes, I have a network use case](useCaseY.html)
|
||||
|
||||
[No, I do not have a network use case](useCaseN.html)
|
||||
|
|
@ -66,13 +66,13 @@ for(tb in tables) {
|
|||
loopTable <- subset(cdmSpecsClean, `CDM Table` == tb)
|
||||
loopTable <- subset(loopTable, select = -c(1))
|
||||
|
||||
print(kable(x = loopTable, align = "l", row.names = FALSE, format = "html") %>%
|
||||
print(kable(x = loopTable, align = "l", row.names = FALSE, format = "html", escape = FALSE) %>%
|
||||
column_spec(1, bold = T) %>%
|
||||
column_spec(2, width = "3in", include_thead = T) %>%
|
||||
column_spec(3, width = "4in", include_thead = T) %>%
|
||||
column_spec(4:10, width = "1in", include_thead = T) %>%
|
||||
kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13))
|
||||
|
||||
# column_spec(2, width = "3in", include_thead = T) %>%
|
||||
# column_spec(3, width = "4in", include_thead = T) %>%
|
||||
# column_spec(4:9, width = "1in", include_thead = T) %>%
|
||||
kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13))
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -232,178 +232,172 @@ GROUP BY person_id
|
|||
|
||||
### Drug Eras
|
||||
|
||||
If the DRUG_EXPOSURE table is populated this script will string together periods of time that a person is exposed to an active drug ingredient, allowing for 30 gaps in between. It will then insert the resulting era records into the DRUG_ERA table. **NOTE** This query only works with 5.3 and below.
|
||||
If the DRUG_EXPOSURE table is populated this script will string together periods of time that a person is exposed to an active drug ingredient, allowing for 30 gaps in between. It will then insert the resulting era records into the DRUG_ERA table. **NOTE** This query only works with the **version 5** series and below.
|
||||
|
||||
```{sql eval = FALSE, echo = TRUE}
|
||||
|
||||
/****************************************************
|
||||
OHDSI-SQL File Instructions
|
||||
-----------------------------
|
||||
1. Set parameter name of schema that contains CDMv4 instance
|
||||
(@SOURCE_CDMV4, @SOURCE_CDMV4_SCHEMA)
|
||||
2. Set parameter name of schema that contains CDMv5 instance
|
||||
(@TARGET_CDMV5, @TARGET_CDMV5_SCHEMA)
|
||||
3. Run this script through SqlRender to produce a script that will work in your
|
||||
source dialect. SqlRender can be found here: https://github.com/OHDSI/SqlRender
|
||||
4. Run the script produced by SQL Render on your target RDBDMS.
|
||||
<RDBMS> File Instructions
|
||||
-------------------------
|
||||
1. This script will hold a number of placeholders for your CDM V4 and CDMV5
|
||||
database/schema. In order to make this file work in your environment, you
|
||||
should plan to do a global "FIND AND REPLACE" on this file to fill in the
|
||||
file with values that pertain to your environment. The following are the
|
||||
tokens you should use when doing your "FIND AND REPLACE" operation:
|
||||
|
||||
[CDM]
|
||||
[CDM].[CDMSCHEMA]
|
||||
|
||||
*********************************************************************************/
|
||||
/* SCRIPT PARAMETERS */
|
||||
|
||||
|
||||
{DEFAULT @TARGET_CDMV5 = '[CDM]' } -- The target CDMv5 database name
|
||||
{DEFAULT @TARGET_CDMV5_SCHEMA = '[CDM].[CDMSCHEMA]' } -- the target CDMv5 database plus schema
|
||||
|
||||
USE @TARGET_CDMV5;
|
||||
-- Code taken from:
|
||||
-- https://github.com/OHDSI/ETL-CMS/blob/master/SQL/create_CDMv5_drug_era_non_stockpile.sql
|
||||
|
||||
|
||||
if object_id('tempdb..#tmp_de', 'U') is not null drop table #tmp_de;
|
||||
|
||||
/****
|
||||
DRUG ERA
|
||||
Note: Eras derived from DRUG_EXPOSURE table, using 30d gap
|
||||
****/
|
||||
IF OBJECT_ID('tempdb..#cteDrugTarget', 'U') IS NOT NULL
|
||||
DROP TABLE #cteDrugTarget;
|
||||
WITH
|
||||
ctePreDrugTarget(drug_exposure_id, person_id, ingredient_concept_id, drug_exposure_start_date, days_supply, drug_exposure_end_date) AS
|
||||
(-- Normalize DRUG_EXPOSURE_END_DATE to either the existing drug exposure end date, or add days supply, or add 1 day to the start date
|
||||
SELECT
|
||||
d.drug_exposure_id
|
||||
, d.person_id
|
||||
, c.concept_id AS ingredient_concept_id
|
||||
, d.drug_exposure_start_date AS drug_exposure_start_date
|
||||
, d.days_supply AS days_supply
|
||||
, COALESCE(
|
||||
---NULLIF returns NULL if both values are the same, otherwise it returns the first parameter
|
||||
NULLIF(drug_exposure_end_date, NULL),
|
||||
---If drug_exposure_end_date != NULL, return drug_exposure_end_date, otherwise go to next case
|
||||
NULLIF(dateadd(day,days_supply,drug_exposure_start_date), drug_exposure_start_date),
|
||||
---If days_supply != NULL or 0, return drug_exposure_start_date + days_supply, otherwise go to next case
|
||||
dateadd(day,1,drug_exposure_start_date)
|
||||
---Add 1 day to the drug_exposure_start_date since there is no end_date or INTERVAL for the days_supply
|
||||
) AS drug_exposure_end_date
|
||||
FROM @cdm_schema.drug_exposure d
|
||||
JOIN @cdm_schema.concept_ancestor ca ON ca.descendant_concept_id = d.drug_concept_id
|
||||
JOIN @cdm_schema.concept c ON ca.ancestor_concept_id = c.concept_id
|
||||
WHERE c.vocabulary_id = 'RxNorm' ---8 selects RxNorm from the vocabulary_id
|
||||
AND c.concept_class_id = 'Ingredient'
|
||||
AND d.drug_concept_id != 0 ---Our unmapped drug_concept_id's are set to 0, so we don't want different drugs wrapped up in the same era
|
||||
AND coalesce(d.days_supply,0) >= 0 ---We have cases where days_supply is negative, and this can set the end_date before the start_date, which we don't want. So we're just looking over those rows. This is a data-quality issue.
|
||||
)
|
||||
|
||||
/* / */
|
||||
|
||||
-- Normalize DRUG_EXPOSURE_END_DATE to either the existing drug exposure end date, or add days supply, or add 1 day to the start date
|
||||
SELECT d.DRUG_EXPOSURE_ID
|
||||
,d.PERSON_ID
|
||||
,c.CONCEPT_ID
|
||||
,d.DRUG_TYPE_CONCEPT_ID
|
||||
,DRUG_EXPOSURE_START_DATE
|
||||
,COALESCE(DRUG_EXPOSURE_END_DATE, DATEADD(day, DAYS_SUPPLY, DRUG_EXPOSURE_START_DATE), DATEADD(day, 1, DRUG_EXPOSURE_START_DATE)) AS DRUG_EXPOSURE_END_DATE
|
||||
,c.CONCEPT_ID AS INGREDIENT_CONCEPT_ID
|
||||
INTO #cteDrugTarget
|
||||
FROM @TARGET_CDMV5_SCHEMA.DRUG_EXPOSURE d
|
||||
INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
|
||||
INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
|
||||
WHERE c.DOMAIN_ID = 'Drug'
|
||||
AND c.CONCEPT_CLASS_ID = 'Ingredient'
|
||||
AND c.STANDARD_CONCEPT = 'S';
|
||||
|
||||
/* / */
|
||||
|
||||
IF OBJECT_ID('tempdb..#cteEndDates', 'U') IS NOT NULL
|
||||
DROP TABLE #cteEndDates;
|
||||
|
||||
/* / */
|
||||
|
||||
SELECT PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,DATEADD(day, - 30, EVENT_DATE) AS END_DATE -- unpad the end date
|
||||
INTO #cteEndDates
|
||||
FROM (
|
||||
SELECT E1.PERSON_ID
|
||||
,E1.INGREDIENT_CONCEPT_ID
|
||||
,E1.EVENT_DATE
|
||||
,COALESCE(E1.START_ORDINAL, MAX(E2.START_ORDINAL)) START_ORDINAL
|
||||
,E1.OVERALL_ORD
|
||||
FROM (
|
||||
SELECT PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,EVENT_DATE
|
||||
,EVENT_TYPE
|
||||
,START_ORDINAL
|
||||
,ROW_NUMBER() OVER (
|
||||
PARTITION BY PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID ORDER BY EVENT_DATE
|
||||
,EVENT_TYPE
|
||||
) AS OVERALL_ORD -- this re-numbers the inner UNION so all rows are numbered ordered by the event date
|
||||
, cteSubExposureEndDates (person_id, ingredient_concept_id, end_date) AS --- A preliminary sorting that groups all of the overlapping exposures into one exposure so that we don't double-count non-gap-days
|
||||
(
|
||||
SELECT person_id, ingredient_concept_id, event_date AS end_date
|
||||
FROM
|
||||
(
|
||||
SELECT person_id, ingredient_concept_id, event_date, event_type,
|
||||
MAX(start_ordinal) OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY event_date, event_type ROWS unbounded preceding) AS start_ordinal,
|
||||
-- this pulls the current START down from the prior rows so that the NULLs
|
||||
-- from the END DATES will contain a value we can compare with
|
||||
ROW_NUMBER() OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY event_date, event_type) AS overall_ord
|
||||
-- this re-numbers the inner UNION so all rows are numbered ordered by the event date
|
||||
FROM (
|
||||
-- select the start dates, assigning a row number to each
|
||||
SELECT PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,DRUG_EXPOSURE_START_DATE AS EVENT_DATE
|
||||
,0 AS EVENT_TYPE
|
||||
,ROW_NUMBER() OVER (
|
||||
PARTITION BY PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM #cteDrugTarget
|
||||
SELECT person_id, ingredient_concept_id, drug_exposure_start_date AS event_date,
|
||||
-1 AS event_type,
|
||||
ROW_NUMBER() OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY drug_exposure_start_date) AS start_ordinal
|
||||
FROM ctePreDrugTarget
|
||||
|
||||
UNION ALL
|
||||
|
||||
-- add the end dates with NULL as the row number, padding the end dates by 30 to allow a grace period for overlapping ranges.
|
||||
SELECT PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,DATEADD(day, 30, DRUG_EXPOSURE_END_DATE)
|
||||
,1 AS EVENT_TYPE
|
||||
,NULL
|
||||
FROM #cteDrugTarget
|
||||
) RAWDATA
|
||||
) E1
|
||||
INNER JOIN (
|
||||
SELECT PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,DRUG_EXPOSURE_START_DATE AS EVENT_DATE
|
||||
,ROW_NUMBER() OVER (
|
||||
PARTITION BY PERSON_ID
|
||||
,INGREDIENT_CONCEPT_ID ORDER BY DRUG_EXPOSURE_START_DATE
|
||||
) AS START_ORDINAL
|
||||
FROM #cteDrugTarget
|
||||
) E2 ON E1.PERSON_ID = E2.PERSON_ID
|
||||
AND E1.INGREDIENT_CONCEPT_ID = E2.INGREDIENT_CONCEPT_ID
|
||||
AND E2.EVENT_DATE <= E1.EVENT_DATE
|
||||
GROUP BY E1.PERSON_ID
|
||||
,E1.INGREDIENT_CONCEPT_ID
|
||||
,E1.EVENT_DATE
|
||||
,E1.START_ORDINAL
|
||||
,E1.OVERALL_ORD
|
||||
) E
|
||||
WHERE 2 * E.START_ORDINAL - E.OVERALL_ORD = 0;
|
||||
SELECT person_id, ingredient_concept_id, drug_exposure_end_date, 1 AS event_type, NULL
|
||||
FROM ctePreDrugTarget
|
||||
) RAWDATA
|
||||
) e
|
||||
WHERE (2 * e.start_ordinal) - e.overall_ord = 0
|
||||
)
|
||||
|
||||
/* / */
|
||||
, cteDrugExposureEnds (person_id, drug_concept_id, drug_exposure_start_date, drug_sub_exposure_end_date) AS
|
||||
(
|
||||
SELECT
|
||||
dt.person_id
|
||||
, dt.ingredient_concept_id
|
||||
, dt.drug_exposure_start_date
|
||||
, MIN(e.end_date) AS drug_sub_exposure_end_date
|
||||
FROM ctePreDrugTarget dt
|
||||
JOIN cteSubExposureEndDates e ON dt.person_id = e.person_id AND dt.ingredient_concept_id = e.ingredient_concept_id AND e.end_date >= dt.drug_exposure_start_date
|
||||
GROUP BY
|
||||
dt.drug_exposure_id
|
||||
, dt.person_id
|
||||
, dt.ingredient_concept_id
|
||||
, dt.drug_exposure_start_date
|
||||
)
|
||||
--------------------------------------------------------------------------------------------------------------
|
||||
, cteSubExposures(row_number, person_id, drug_concept_id, drug_sub_exposure_start_date, drug_sub_exposure_end_date, drug_exposure_count) AS
|
||||
(
|
||||
SELECT ROW_NUMBER() OVER (PARTITION BY person_id, drug_concept_id, drug_sub_exposure_end_date ORDER BY person_id)
|
||||
, person_id, drug_concept_id, MIN(drug_exposure_start_date) AS drug_sub_exposure_start_date, drug_sub_exposure_end_date, COUNT(*) AS drug_exposure_count
|
||||
FROM cteDrugExposureEnds
|
||||
GROUP BY person_id, drug_concept_id, drug_sub_exposure_end_date
|
||||
--ORDER BY person_id, drug_concept_id
|
||||
)
|
||||
--------------------------------------------------------------------------------------------------------------
|
||||
/*Everything above grouped exposures into sub_exposures if there was overlap between exposures.
|
||||
*So there was no persistence window. Now we can add the persistence window to calculate eras.
|
||||
*/
|
||||
--------------------------------------------------------------------------------------------------------------
|
||||
, cteFinalTarget(row_number, person_id, ingredient_concept_id, drug_sub_exposure_start_date, drug_sub_exposure_end_date, drug_exposure_count, days_exposed) AS
|
||||
(
|
||||
SELECT row_number, person_id, drug_concept_id, drug_sub_exposure_start_date, drug_sub_exposure_end_date, drug_exposure_count
|
||||
, datediff(day,drug_sub_exposure_start_date,drug_sub_exposure_end_date) AS days_exposed
|
||||
FROM cteSubExposures
|
||||
)
|
||||
--------------------------------------------------------------------------------------------------------------
|
||||
, cteEndDates (person_id, ingredient_concept_id, end_date) AS -- the magic
|
||||
(
|
||||
SELECT person_id, ingredient_concept_id, dateadd(day,-30,event_date) AS end_date -- unpad the end date
|
||||
FROM
|
||||
(
|
||||
SELECT person_id, ingredient_concept_id, event_date, event_type,
|
||||
MAX(start_ordinal) OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY event_date, event_type ROWS UNBOUNDED PRECEDING) AS start_ordinal,
|
||||
-- this pulls the current START down from the prior rows so that the NULLs
|
||||
-- from the END DATES will contain a value we can compare with
|
||||
ROW_NUMBER() OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY event_date, event_type) AS overall_ord
|
||||
-- this re-numbers the inner UNION so all rows are numbered ordered by the event date
|
||||
FROM (
|
||||
-- select the start dates, assigning a row number to each
|
||||
SELECT person_id, ingredient_concept_id, drug_sub_exposure_start_date AS event_date,
|
||||
-1 AS event_type,
|
||||
ROW_NUMBER() OVER (PARTITION BY person_id, ingredient_concept_id
|
||||
ORDER BY drug_sub_exposure_start_date) AS start_ordinal
|
||||
FROM cteFinalTarget
|
||||
|
||||
IF OBJECT_ID('tempdb..#cteDrugExpEnds', 'U') IS NOT NULL
|
||||
DROP TABLE #cteDrugExpEnds;
|
||||
UNION ALL
|
||||
|
||||
/* / */
|
||||
-- pad the end dates by 30 to allow a grace period for overlapping ranges.
|
||||
SELECT person_id, ingredient_concept_id, dateadd(day,30,drug_sub_exposure_end_date), 1 AS event_type, NULL
|
||||
FROM cteFinalTarget
|
||||
) RAWDATA
|
||||
) e
|
||||
WHERE (2 * e.start_ordinal) - e.overall_ord = 0
|
||||
|
||||
SELECT d.PERSON_ID
|
||||
,d.INGREDIENT_CONCEPT_ID
|
||||
,d.DRUG_TYPE_CONCEPT_ID
|
||||
,d.DRUG_EXPOSURE_START_DATE
|
||||
,MIN(e.END_DATE) AS ERA_END_DATE
|
||||
INTO #cteDrugExpEnds
|
||||
FROM #cteDrugTarget d
|
||||
INNER JOIN #cteEndDates e ON d.PERSON_ID = e.PERSON_ID
|
||||
AND d.INGREDIENT_CONCEPT_ID = e.INGREDIENT_CONCEPT_ID
|
||||
AND e.END_DATE >= d.DRUG_EXPOSURE_START_DATE
|
||||
GROUP BY d.PERSON_ID
|
||||
,d.INGREDIENT_CONCEPT_ID
|
||||
,d.DRUG_TYPE_CONCEPT_ID
|
||||
,d.DRUG_EXPOSURE_START_DATE;
|
||||
|
||||
/* / */
|
||||
|
||||
INSERT INTO @TARGET_CDMV5_SCHEMA.drug_era
|
||||
SELECT row_number() OVER (
|
||||
ORDER BY person_id
|
||||
) AS drug_era_id
|
||||
,person_id
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,min(DRUG_EXPOSURE_START_DATE) AS drug_era_start_date
|
||||
,ERA_END_DATE
|
||||
,COUNT(*) AS DRUG_EXPOSURE_COUNT
|
||||
,30 AS gap_days
|
||||
FROM #cteDrugExpEnds
|
||||
GROUP BY person_id
|
||||
,INGREDIENT_CONCEPT_ID
|
||||
,drug_type_concept_id
|
||||
,ERA_END_DATE;
|
||||
)
|
||||
, cteDrugEraEnds (person_id, drug_concept_id, drug_sub_exposure_start_date, drug_era_end_date, drug_exposure_count, days_exposed) AS
|
||||
(
|
||||
SELECT
|
||||
ft.person_id
|
||||
, ft.ingredient_concept_id
|
||||
, ft.drug_sub_exposure_start_date
|
||||
, MIN(e.end_date) AS era_end_date
|
||||
, drug_exposure_count
|
||||
, days_exposed
|
||||
FROM cteFinalTarget ft
|
||||
JOIN cteEndDates e ON ft.person_id = e.person_id AND ft.ingredient_concept_id = e.ingredient_concept_id AND e.end_date >= ft.drug_sub_exposure_start_date
|
||||
GROUP BY
|
||||
ft.person_id
|
||||
, ft.ingredient_concept_id
|
||||
, ft.drug_sub_exposure_start_date
|
||||
, drug_exposure_count
|
||||
, days_exposed
|
||||
)
|
||||
SELECT
|
||||
row_number()over(order by person_id) drug_era_id
|
||||
, person_id
|
||||
, drug_concept_id
|
||||
, MIN(drug_sub_exposure_start_date) AS drug_era_start_date
|
||||
, drug_era_end_date
|
||||
, SUM(drug_exposure_count) AS drug_exposure_count
|
||||
, datediff(day,MIN(drug_sub_exposure_start_date),drug_era_end_date)-SUM(days_exposed) as gap_days
|
||||
INTO #tmp_de
|
||||
FROM cteDrugEraEnds dee
|
||||
GROUP BY person_id, drug_concept_id, drug_era_end_date;
|
||||
|
||||
INSERT INTO @cdm_schema.drug_era(drug_era_id,person_id, drug_concept_id, drug_era_start_date, drug_era_end_date, drug_exposure_count, gap_days)
|
||||
SELECT * FROM #tmp_de;
|
||||
```
|
||||
|
||||
## **Example ETL Script**
|
||||
|
|
|
|||
|
|
@ -0,0 +1,10 @@
|
|||
---
|
||||
title: "Local Data"
|
||||
output: html_document
|
||||
---
|
||||
|
||||
Okay, so you don't have a network use case. **Is this data element specific to your data source, or are there others in the community who might also have this data but don't yet need it for a study or data model convention?**
|
||||
|
||||
[Yes, this element is specific to my data source](localChange.html)
|
||||
|
||||
[No, there are others in the community who also have this data](leaveAsIs.html)
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
---
|
||||
title: "OMOP Vocabulary"
|
||||
output: html_document
|
||||
---
|
||||
|
||||
Great, you have a network use case!
|
||||
|
||||
Next question: **Is there an existing OMOP vocabulary to support this new element? If you are unsure, feel free to check [Athena](https://athena.ohdsi.org/search-terms/terms?query).**
|
||||
|
||||
[Yes, I have all the required vocabulary I need](vocabY.html)
|
||||
|
||||
[No, I there is not an existing OMOP vocabulary to support my request](vocabN.html)
|
||||
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
---
|
||||
title: "Open Source Vocabulary"
|
||||
output: html_document
|
||||
---
|
||||
|
||||
Okay, so you have a use case but you don't have an OMOP vocabulary to support your need. **Is there an existing open-source (not proprietary or custom) vocabulary that has not yet been incorporated into the OMOP vocabulary?**
|
||||
|
||||
[Yes, the vocabulary exists, it just needs to be brought in](vocabRequest.html)
|
||||
|
||||
[No, there is no open-source vocabulary for this data element](contactVocab.html)
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
---
|
||||
title: "Vocabulary Request"
|
||||
output: html_document
|
||||
---
|
||||
|
||||
Okay so you have something you would like to add to the CDM and there is an existing OMOP vocabulary we can bring in to support it. **In this case, please open an issue on the vocabulary github with the details of what you need added** as data elements in the CDM must have a vocabulary in place before they can be implemented. The team will follow up with you should they need additional information.
|
||||
|
||||
[Vocabulary GitHub Issue Tracker](https://github.com/OHDSI/Vocabulary-v5.0/issues)
|
||||
|
||||
Once that request is made, please follow the [CDM Request Process](cdmRequestProcess.html) to begin the steps soliciting a change or addition to the model itself. Need more guidance? Consider contacting the CDM Working Group on our [GitHub](https://github.com/OHDSI/CommonDataModel) or [Teams Channel](https://teams.microsoft.com/l/team/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/conversations?groupId=a6f2c516-e568-4974-8f1e-a7bdc2f997c5&tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5).
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
---
|
||||
title: "Request Process"
|
||||
output: html_document
|
||||
---
|
||||
|
||||
Great, so you have a network use case and an existing OMOP Vocabulary! **From here, please follow the steps to formally request a change to the OMOP Common Data Model.**
|
||||
|
||||
[CDM Request Process](cdmRequestProcess.html)
|
||||
Loading…
Reference in New Issue