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Adds vocab option to decision tree

This commit is contained in:
Clair Blacketer 2022-07-26 21:48:28 -04:00
parent 468eca3571
commit e2d337ce79
29 changed files with 874 additions and 852 deletions
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32
docs/background.html
View File

@ -13,7 +13,7 @@
<title>background.knit</title> <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> <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" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <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" /> <link rel="stylesheet" href="style.css" type="text/css" />
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -312,7 +316,7 @@ div.tocify {
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
<div class="navbar-header"> <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> <span class="icon-bar"></span>
<span class="icon-bar"></span> <span class="icon-bar"></span>
@ -328,7 +332,7 @@ div.tocify {
</a> </a>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-landmark"></span>
Background Background
@ -348,7 +352,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -368,7 +372,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -386,7 +390,7 @@ div.tocify {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -399,19 +403,22 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -421,7 +428,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-question"></span>
How to How to
@ -441,7 +448,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-life-ring"></span>
Support Support
@ -449,6 +456,9 @@ div.tocify {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

32
docs/cdm30.html
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@ -13,7 +13,7 @@
<title>CDM v3</title> <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> <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" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <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" /> <link rel="stylesheet" href="style.css" type="text/css" />
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -312,7 +316,7 @@ div.tocify {
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
<div class="navbar-header"> <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> <span class="icon-bar"></span>
<span class="icon-bar"></span> <span class="icon-bar"></span>
@ -328,7 +332,7 @@ div.tocify {
</a> </a>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-landmark"></span>
Background Background
@ -348,7 +352,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -368,7 +372,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -386,7 +390,7 @@ div.tocify {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -399,19 +403,22 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -421,7 +428,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-question"></span>
How to How to
@ -441,7 +448,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-life-ring"></span>
Support Support
@ -449,6 +456,9 @@ div.tocify {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

8
docs/cdm53.html
View File

@ -406,11 +406,14 @@ div.tocify {
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" 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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
@ -453,6 +456,9 @@ div.tocify {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

32
docs/cdm531.html
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@ -13,7 +13,7 @@
<title>OMOP CDM v5.3.1</title> <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> <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" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <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" /> <link rel="stylesheet" href="style.css" type="text/css" />
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -312,7 +316,7 @@ div.tocify {
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
<div class="navbar-header"> <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> <span class="icon-bar"></span>
<span class="icon-bar"></span> <span class="icon-bar"></span>
@ -328,7 +332,7 @@ div.tocify {
</a> </a>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-landmark"></span>
Background Background
@ -348,7 +352,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -368,7 +372,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -386,7 +390,7 @@ div.tocify {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -399,19 +403,22 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -421,7 +428,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-question"></span>
How to How to
@ -441,7 +448,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-life-ring"></span>
Support Support
@ -449,6 +456,9 @@ div.tocify {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

8
docs/cdm54.html
View File

@ -406,11 +406,14 @@ div.tocify {
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" 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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
@ -453,6 +456,9 @@ div.tocify {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

32
docs/cdm54Changes.html
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@ -13,7 +13,7 @@
<title>Changes by Table</title> <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>
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<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
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@ -419,9 +419,9 @@ $(document).ready(function () {
<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>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 have a documented network use case for this data? 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><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="useCaseY.html">Yes, I have a network use case</a></p> <p><a href="networkUseCase.html">I think I need to change the OMOP CDM</a></p>
<p><a href="useCaseN.html">No, I do not have a network use case</a></p> <p><a href="vocabN.html">I need vocabulary support</a></p>

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@ -13,7 +13,7 @@
<title>Preserving Privacy in an OMOP CDM Implementation</title> <title>Preserving Privacy in an OMOP CDM Implementation</title>
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@ -13,7 +13,7 @@
<title>CDM R Package Demo</title> <title>CDM R Package Demo</title>
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@ -519,7 +519,7 @@ div.tocify {
<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>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> <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> </ol>
<p>Once the document is ready to submit, please email <a href="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> <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> <ul>
<li>Proposal merits further review (move on to next steps)</li> <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 <li>Proposal is not ready for workgroup review due to one or more factors

32
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@ -13,7 +13,7 @@
<title>Ask A Question</title> <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> <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" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <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" /> <link rel="stylesheet" href="style.css" type="text/css" />
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summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
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<span class="icon-bar"></span> <span class="icon-bar"></span>
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</a> </a>
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@ -348,7 +352,7 @@ div.tocify {
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@ -368,7 +372,7 @@ div.tocify {
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CDM Versions CDM Versions
@ -386,7 +390,7 @@ div.tocify {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
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<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -399,19 +403,22 @@ div.tocify {
</ul> </ul>
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<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
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<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
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<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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -421,7 +428,7 @@ div.tocify {
</ul> </ul>
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@ -441,7 +448,7 @@ div.tocify {
</ul> </ul>
</li> </li>
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<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">
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<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

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@ -13,7 +13,7 @@
<title>dataModelConventions.knit</title> <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>
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<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <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" /> <link rel="stylesheet" href="style.css" type="text/css" />
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summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -312,7 +316,7 @@ div.tocify {
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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<div class="navbar-header"> <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">
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@ -328,7 +332,7 @@ div.tocify {
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@ -348,7 +352,7 @@ div.tocify {
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@ -368,7 +372,7 @@ div.tocify {
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CDM Versions CDM Versions
@ -386,7 +390,7 @@ div.tocify {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
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<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"> <ul class="dropdown-menu" role="menu">
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<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -399,19 +403,22 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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">
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Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
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<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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -421,7 +428,7 @@ div.tocify {
</ul> </ul>
</li> </li>
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@ -441,7 +448,7 @@ div.tocify {
</ul> </ul>
</li> </li>
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<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">
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@ -449,6 +456,9 @@ div.tocify {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

32
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@ -13,7 +13,7 @@
<title>Download</title> <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> <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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<link rel="stylesheet" href="style.css" type="text/css" /> <link rel="stylesheet" href="style.css" type="text/css" />
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summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
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<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">
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@ -328,7 +332,7 @@ div.tocify {
</a> </a>
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@ -348,7 +352,7 @@ div.tocify {
</ul> </ul>
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<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">
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@ -368,7 +372,7 @@ div.tocify {
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@ -386,7 +390,7 @@ div.tocify {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
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<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -399,19 +403,22 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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">
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<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -421,7 +428,7 @@ div.tocify {
</ul> </ul>
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@ -441,7 +448,7 @@ div.tocify {
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@ -15,7 +15,7 @@
<title>drug_dose.knit</title> <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> <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" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
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<link rel="stylesheet" href="style.css" type="text/css" /> <link rel="stylesheet" href="style.css" type="text/css" />
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summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -238,7 +242,7 @@ $(document).ready(function () {
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<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">
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@ -254,7 +258,7 @@ $(document).ready(function () {
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<li class="dropdown"> <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> <span class="fa fa-landmark"></span>
Background Background
@ -274,7 +278,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -294,7 +298,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -312,7 +316,7 @@ $(document).ready(function () {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -325,19 +329,22 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -347,7 +354,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-question"></span>
How to How to
@ -367,7 +374,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-life-ring"></span>
Support Support
@ -375,6 +382,9 @@ $(document).ready(function () {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

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@ -13,7 +13,7 @@
<title>Observation Period Considerations for EHR Data</title> <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> <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" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <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" /> <link rel="stylesheet" href="style.css" type="text/css" />
@ -85,6 +86,9 @@ button.code-folding-btn:focus {
summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -236,7 +240,7 @@ $(document).ready(function () {
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
<div class="navbar-header"> <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> <span class="icon-bar"></span>
<span class="icon-bar"></span> <span class="icon-bar"></span>
@ -252,7 +256,7 @@ $(document).ready(function () {
</a> </a>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-landmark"></span>
Background Background
@ -272,7 +276,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -292,7 +296,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -310,7 +314,7 @@ $(document).ready(function () {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -323,19 +327,22 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -345,7 +352,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-question"></span>
How to How to
@ -365,7 +372,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-life-ring"></span>
Support Support
@ -373,6 +380,9 @@ $(document).ready(function () {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

8
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View File

@ -406,11 +406,14 @@ div.tocify {
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" 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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
@ -453,6 +456,9 @@ div.tocify {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

10
docs/index.html
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@ -330,11 +330,14 @@ $(document).ready(function () {
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" 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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
@ -377,6 +380,9 @@ $(document).ready(function () {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>
@ -501,7 +507,7 @@ $(document).ready(function () {
<div id="meeting-information" class="section level3"> <div id="meeting-information" class="section level3">
<h3>Meeting Information</h3> <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>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>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 <a href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu">this form</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>

32
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@ -13,7 +13,7 @@
<title>Indices, Primary Keys and Foreign Key Constraints</title> <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> <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" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <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" /> <link rel="stylesheet" href="style.css" type="text/css" />
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -312,7 +316,7 @@ div.tocify {
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
<div class="navbar-header"> <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> <span class="icon-bar"></span>
<span class="icon-bar"></span> <span class="icon-bar"></span>
@ -328,7 +332,7 @@ div.tocify {
</a> </a>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-landmark"></span>
Background Background
@ -348,7 +352,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -368,7 +372,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -386,7 +390,7 @@ div.tocify {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -399,19 +403,22 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -421,7 +428,7 @@ div.tocify {
</ul> </ul>
</li> </li>
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<h1 class="title toc-ignore">Network Use Case</h1>
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<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>
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<title>Oncology Extension</title> <title>Oncology Extension</title>
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@ -486,429 +496,14 @@ div.tocify {
<h2>OMOP Common Data Model Oncology Extension Documentation</h2> <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>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> <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 &#39;../inst/csv/ <pre><code>## Warning in read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found
## OMOP_CDM_Oncology_Ex_Table_Level.csv&#39;</code></pre> ## by readTableHeader on &#39;../inst/csv/OMOP_CDM_Oncology_Ex_Table_Level.csv&#39;</code></pre>
<div id="episode" class="section level3 tabset tabset-pills"> <div id="episode" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">EPISODE</h3> <h3 class="tabset tabset-pills">EPISODE</h3>
<p><strong>Table Description</strong></p> <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>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><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> <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&amp;page=1&amp;pageSize=15&amp;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&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;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>
<div id="episode_event" class="section level3 tabset tabset-pills"> <div id="episode_event" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">EPISODE_EVENT</h3> <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>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><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> <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&amp;conceptClass=Field&amp;page=1&amp;pageSize=15&amp;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>
<div id="measurement" class="section level3 tabset tabset-pills"> <div id="measurement" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">MEASUREMENT</h3> <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>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><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> <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&amp;conceptClass=Field&amp;page=1&amp;pageSize=15&amp;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>
</div> </div>

32
docs/queries.html
View File

@ -15,7 +15,7 @@
<title>Example_Queries</title> <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> <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" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <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" /> <link rel="stylesheet" href="style.css" type="text/css" />
@ -87,6 +88,9 @@ button.code-folding-btn:focus {
summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -238,7 +242,7 @@ $(document).ready(function () {
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
<div class="navbar-header"> <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> <span class="icon-bar"></span>
<span class="icon-bar"></span> <span class="icon-bar"></span>
@ -254,7 +258,7 @@ $(document).ready(function () {
</a> </a>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-landmark"></span>
Background Background
@ -274,7 +278,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -294,7 +298,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -312,7 +316,7 @@ $(document).ready(function () {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -325,19 +329,22 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -347,7 +354,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-question"></span>
How to How to
@ -367,7 +374,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-life-ring"></span>
Support Support
@ -375,6 +382,9 @@ $(document).ready(function () {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

32
docs/reviewProposals.html
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@ -13,7 +13,7 @@
<title>CDM Proposals Under Review</title> <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> <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" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <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" /> <link rel="stylesheet" href="style.css" type="text/css" />
@ -85,6 +86,9 @@ button.code-folding-btn:focus {
summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -236,7 +240,7 @@ $(document).ready(function () {
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
<div class="navbar-header"> <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> <span class="icon-bar"></span>
<span class="icon-bar"></span> <span class="icon-bar"></span>
@ -252,7 +256,7 @@ $(document).ready(function () {
</a> </a>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-landmark"></span>
Background Background
@ -272,7 +276,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -292,7 +296,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -310,7 +314,7 @@ $(document).ready(function () {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -323,19 +327,22 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -345,7 +352,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-question"></span>
How to How to
@ -365,7 +372,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-life-ring"></span>
Support Support
@ -373,6 +380,9 @@ $(document).ready(function () {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

12
docs/site_libs/header-attrs-2.11/header-attrs.js
View File

@ -1,12 +0,0 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

10
docs/sqlScripts.html
View File

@ -406,11 +406,14 @@ div.tocify {
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" 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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
@ -453,6 +456,9 @@ div.tocify {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>
@ -702,7 +708,7 @@ GROUP BY person_id
</div> </div>
<div id="drug-eras" class="section level3"> <div id="drug-eras" class="section level3">
<h3>Drug Eras</h3> <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> <pre class="sql"><code>
-- Code taken from: -- Code taken from:
-- https://github.com/OHDSI/ETL-CMS/blob/master/SQL/create_CDMv5_drug_era_non_stockpile.sql -- https://github.com/OHDSI/ETL-CMS/blob/master/SQL/create_CDMv5_drug_era_non_stockpile.sql

32
docs/vocabulary.html
View File

@ -13,7 +13,7 @@
<title>How the Vocabulary is Built</title> <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> <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" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <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" /> <link rel="stylesheet" href="style.css" type="text/css" />
@ -88,6 +89,9 @@ button.code-folding-btn:focus {
summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -312,7 +316,7 @@ div.tocify {
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
<div class="navbar-header"> <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> <span class="icon-bar"></span>
<span class="icon-bar"></span> <span class="icon-bar"></span>
@ -328,7 +332,7 @@ div.tocify {
</a> </a>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-landmark"></span>
Background Background
@ -348,7 +352,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -368,7 +372,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -386,7 +390,7 @@ div.tocify {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -399,19 +403,22 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-plus-square"></span>
Proposals CDM Proposals
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
</li>
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <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"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -421,7 +428,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-question"></span>
How to How to
@ -441,7 +448,7 @@ div.tocify {
</ul> </ul>
</li> </li>
<li class="dropdown"> <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> <span class="fa fa-life-ring"></span>
Support Support
@ -449,6 +456,9 @@ div.tocify {
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li>
<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
</li>
<li> <li>
<a href="faq.html">FAQ</a> <a href="faq.html">FAQ</a>
</li> </li>

6
rmd/cdmDecisionTree.Rmd
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@ -6,8 +6,8 @@ output:
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. 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 have a documented network use case for this data? 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. **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?**
[Yes, I have a network use case](useCaseY.html) [I think I need to change the OMOP CDM](networkUseCase.html)
[No, I do not have a network use case](useCaseN.html) [I need vocabulary support](vocabN.html)

10
rmd/networkUseCase.Rmd Normal file
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@ -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)

12
rmd/oncology.Rmd
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@ -66,13 +66,13 @@ for(tb in tables) {
loopTable <- subset(cdmSpecsClean, `CDM Table` == tb) loopTable <- subset(cdmSpecsClean, `CDM Table` == tb)
loopTable <- subset(loopTable, select = -c(1)) 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(1, bold = T) %>%
column_spec(2, width = "3in", include_thead = T) %>% # column_spec(2, width = "3in", include_thead = T) %>%
column_spec(3, width = "4in", include_thead = T) %>% # column_spec(3, width = "4in", include_thead = T) %>%
column_spec(4:10, width = "1in", 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)) kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13))
} }