mz-health/OMOP
mz-health
/
OMOP
mirror of https://github.com/OHDSI/CommonDataModel.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Fixes to documentation 

Closes #380, #379, #350, #334, #316, #129
This commit is contained in:
Clair Blacketer 2021-02-18 21:37:32 -05:00
parent 7bb9cf23a0
commit 35d53c9f5a
19 changed files with 2058 additions and 37 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

BIN
.DS_Store vendored
View File

Binary file not shown.

17
docs/background.html
View File

@ -368,12 +368,22 @@ div.tocify {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -391,6 +401,9 @@ div.tocify {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>

578
docs/cdm30.html Normal file
View File

@ -0,0 +1,578 @@
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>CDM v3</title>
<script src="site_libs/header-attrs-2.6/header-attrs.js"></script>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
<link rel="stylesheet" href="style.css" type="text/css" />
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 51px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 56px;
margin-top: -56px;
}
.section h2 {
padding-top: 56px;
margin-top: -56px;
}
.section h3 {
padding-top: 56px;
margin-top: -56px;
}
.section h4 {
padding-top: 56px;
margin-top: -56px;
}
.section h5 {
padding-top: 56px;
margin-top: -56px;
}
.section h6 {
padding-top: 56px;
margin-top: -56px;
}
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "&#xe258;";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
}
.tocify .list-group-item {
border-radius: 0px;
}
</style>
</head>
<body>
<div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
<span class="fas fa-list-alt"></span>
Conventions
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
CDM Versions
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>
<li>
<a href="cdm60.html">CDM v6.0</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
Proposals
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="reviewProposals.html">Under Review</a>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="oncology.html">Oncology CDM Proposal</a>
</li>
<li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
</li>
<li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
</li>
</ul>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
Help
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="faq.html">FAQ</a>
</li>
<li>
<a href="contribute.html">Ask a Question</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-wrench"></span>
How to
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="sqlScripts.html">SQL Scripts</a>
</li>
<li>
<a href="download.html">Download the DDL</a>
</li>
<li>
<a href="drug_dose.html">Calculate Drug Dose</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github fa-lg"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">CDM v3</h1>
</div>
<p>You can find the specification for CDM v3 at this <a href="https://forums.ohdsi.org/uploads/default/original/1X/2d8b44ea1ee0f9f70427dd2c7332335b8eb6a073.docx">link</a>.</p>
</div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
});
});
</script>
<!-- code folding -->
<script>
$(document).ready(function () {
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
// establish options
var options = {
selectors: "h1,h2,h3,h4,h5",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
};
options.showAndHide = true;
options.smoothScroll = true;
// tocify
var toc = $("#TOC").tocify(options).data("toc-tocify");
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>

23
docs/cdm531.html
View File

@ -368,12 +368,22 @@ div.tocify {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -391,6 +401,9 @@ div.tocify {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>
@ -4650,7 +4663,7 @@ CONCEPT
unit_concept_id
</td>
<td style="text-align:left;width: 3in; ">
There is currently no vocabulary link between measurement Concepts and unit Concepts, the UNIT_CONCEPT_ID is a representation of the units as provided by the source data after ETL clean up.
There is currently no recommended unit for individual measurements, i.e. it is not mandatory to represent Hemoglobin a1C measurements as a percentage. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data.
</td>
<td style="text-align:left;width: 4in; ">
There is no standardization requirement for units associated with MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit.
@ -5242,7 +5255,7 @@ CONCEPT
unit_concept_id
</td>
<td style="text-align:left;width: 3in; ">
There is currently no vocabulary link between observation Concepts and unit Concepts, the UNIT_CONCEPT_ID is a representation of the units as provided by the source data after ETL clean up.
There is currently no recommended unit for individual observation concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data.
</td>
<td style="text-align:left;width: 4in; ">
There is no standardization requirement for units associated with OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit.
@ -6963,7 +6976,7 @@ No
<div id="fact_relationship" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">FACT_RELATIONSHIP</h3>
<p><strong>Table Description</strong></p>
<p>The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the CDM. Relationships can be defined between facts from the same domain, or different domains. Examples of Fact Relationships include: Person relationships (parent-child), care site relationships (hierarchical organizational structure of facilities within a health system), indication relationship (between drug exposures and associated conditions), usage relationships (of devices during the course of an associated procedure), or facts derived from one another (measurements derived from an associated specimen).</p>
<p>The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the CDM. Relationships can be defined between facts from the same domain, or different domains. Examples of Fact Relationships include: <a href="https://athena.ohdsi.org/search-terms/terms?domain=Relationship&amp;standardConcept=Standard&amp;page=2&amp;pageSize=15&amp;query=">Person relationships</a> (parent-child), care site relationships (hierarchical organizational structure of facilities within a health system), indication relationship (between drug exposures and associated conditions), usage relationships (of devices during the course of an associated procedure), or facts derived from one another (measurements derived from an associated specimen).</p>
<p><strong>ETL Conventions</strong></p>
<p>All relationships are directional, and each relationship is represented twice symmetrically within the FACT_RELATIONSHIP table. For example, two persons if person_id = 1 is the mother of person_id = 2 two records are in the FACT_RELATIONSHIP table (all strings in fact concept_id records in the Concept table: - Person, 1, Person, 2, parent of - Person, 2, Person, 1, child of</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">

25
docs/cdm60.html
View File

@ -368,12 +368,22 @@ div.tocify {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -391,6 +401,9 @@ div.tocify {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>
@ -510,7 +523,7 @@ div.tocify {
<p><strong>User Guide</strong></p>
<p>All records in this table are independent Persons.</p>
<p><strong>ETL Conventions</strong></p>
<p>All Persons in a database needs one record in this table, unless they fail data quality requirements specified in the ETL. Persons with no Events should have a record nonetheless. If more than one data source contributes Events to the database, Persons must be reconciled, if possible, across the sources to create one single record per Person. The BIRTH_DATETIME must be equivalent to the content of BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR. There is a helpful rule listed in table below for how to derive BIRTH_DATETIME if it is not available in the source. <strong>New to CDM v6.0</strong> The person’s death date is now stored in this table instead of the separate DEATH table.</p>
<p>All Persons in a database needs one record in this table, unless they fail data quality requirements specified in the ETL. Persons with no Events should have a record nonetheless. If more than one data source contributes Events to the database, Persons must be reconciled, if possible, across the sources to create one single record per Person. The BIRTH_DATETIME must be equivalent to the content of BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR. There is a helpful rule listed in table below for how to derive BIRTH_DATETIME if it is not available in the source. <strong>New to CDM v6.0</strong> The person’s death date is now stored in this table instead of the separate DEATH table. In the case that multiple dates of death are given in the source data the ETL should make a choice as to which death date to put in the PERSON table. Any additional dates can be stored in the OBSERVATION table using the concept <a href="https://athena.ohdsi.org/search-terms/terms/4265167">4265167</a> which stands for ‘Date of death’ . Similarly, the cause of death is stored in the CONDITION_OCCURRENCE table using the CONDITION_STATUS_CONCEPT_ID <a href="https://athena.ohdsi.org/search-terms/terms/32891">32891</a> for ‘Cause of death’.</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead>
<tr>
@ -4686,7 +4699,7 @@ CONCEPT
unit_concept_id
</td>
<td style="text-align:left;width: 3in; ">
There is currently no vocabulary link between measurement Concepts and unit Concepts, the UNIT_CONCEPT_ID is a representation of the units as provided by the source data after ETL clean up.
There is currently no recommended unit for individual measurements, i.e. it is not mandatory to represent Hemoglobin a1C measurements as a percentage. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data.
</td>
<td style="text-align:left;width: 4in; ">
There is no standardization requirement for units associated with MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit.
@ -5278,7 +5291,7 @@ CONCEPT
unit_concept_id
</td>
<td style="text-align:left;width: 3in; ">
There is currently no vocabulary link between observation Concepts and unit Concepts, the UNIT_CONCEPT_ID is a representation of the units as provided by the source data after ETL clean up.
There is currently no recommended unit for individual observation concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data.
</td>
<td style="text-align:left;width: 4in; ">
There is no standardization requirement for units associated with OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit.
@ -6902,7 +6915,7 @@ No
<div id="fact_relationship" class="section level3 tabset tabset-pills">
<h3 class="tabset tabset-pills">FACT_RELATIONSHIP</h3>
<p><strong>Table Description</strong></p>
<p>The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the CDM. Relationships can be defined between facts from the same domain, or different domains. Examples of Fact Relationships include: Person relationships (parent-child), care site relationships (hierarchical organizational structure of facilities within a health system), indication relationship (between drug exposures and associated conditions), usage relationships (of devices during the course of an associated procedure), or facts derived from one another (measurements derived from an associated specimen).</p>
<p>The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the CDM. Relationships can be defined between facts from the same domain, or different domains. Examples of Fact Relationships include: <a href="https://athena.ohdsi.org/search-terms/terms?domain=Relationship&amp;standardConcept=Standard&amp;page=2&amp;pageSize=15&amp;query=">Person relationships</a> (parent-child), care site relationships (hierarchical organizational structure of facilities within a health system), indication relationship (between drug exposures and associated conditions), usage relationships (of devices during the course of an associated procedure), or facts derived from one another (measurements derived from an associated specimen).</p>
<p><strong>ETL Conventions</strong></p>
<p>All relationships are directional, and each relationship is represented twice symmetrically within the FACT_RELATIONSHIP table. For example, two persons if person_id = 1 is the mother of person_id = 2 two records are in the FACT_RELATIONSHIP table (all strings in fact concept_id records in the Concept table: - Person, 1, Person, 2, parent of - Person, 2, Person, 1, child of</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">

17
docs/contribute.html
View File

@ -368,12 +368,22 @@ div.tocify {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -391,6 +401,9 @@ div.tocify {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>

17
docs/dataModelConventions.html
View File

@ -368,12 +368,22 @@ div.tocify {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -391,6 +401,9 @@ div.tocify {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>

17
docs/download.html
View File

@ -368,12 +368,22 @@ div.tocify {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -391,6 +401,9 @@ div.tocify {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>

17
docs/drug_dose.html
View File

@ -294,12 +294,22 @@ $(document).ready(function () {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -317,6 +327,9 @@ $(document).ready(function () {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>

17
docs/faq.html
View File

@ -292,12 +292,22 @@ $(document).ready(function () {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -315,6 +325,9 @@ $(document).ready(function () {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>

BIN
docs/images/diabetes-related_case.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 129 KiB

BIN
docs/images/mapping_of_concepts.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 326 KiB

BIN
docs/images/pregnancy-related_case.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 138 KiB

17
docs/index.html
View File

@ -292,12 +292,22 @@ $(document).ready(function () {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -315,6 +325,9 @@ $(document).ready(function () {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>

17
docs/oncology.html
View File

@ -368,12 +368,22 @@ div.tocify {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -391,6 +401,9 @@ div.tocify {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>

19
docs/queries.html
View File

@ -294,12 +294,22 @@ $(document).ready(function () {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -317,6 +327,9 @@ $(document).ready(function () {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>
@ -414,7 +427,7 @@ $(document).ready(function () {
</div>
<p>discuss top-level visit query</p>
<p>The query below will find all standard concepts in the Visit domain that do not have any ancestors. These are considered “top-level” visit concepts and can be used to define categories of visits in cohort definitions. For example, the Inpatient Visit concept <a href="https://athena.ohdsi.org/search-terms/terms/9201">9201</a> subsumes the concepts for Inpatient Hospital and Inpatient in Psychiatric Facility. Instead of creating a concept set with all of these terms to define an inpatient visit you can use 9201 and all of it’s descendants, a concept found using the top-level query.</p>
<p>WITH top_level AS (SELECT concept_id, concept_name FROM concept LEFT JOIN concept_ancestor ON concept_id=descendant_concept_id AND ancestor_concept_id!=descendant_concept_id WHERE domain_id=‘Visit’ AND standard_concept=‘S’ AND ancestor_concept_id IS NULL ) SELECT top_level.concept_id, top_level.concept_name, descendant.concept_id, descendant.concept_name FROM concept_ancestor JOIN top_level ON top_level.concept_id = ancestor_concept_id JOIN concept descendant ON descendant.concept_id = descendant_concept_id WHERE descendant.domain_id = ‘Visit’;</p>

17
docs/reviewProposals.html
View File

@ -292,12 +292,22 @@ $(document).ready(function () {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -315,6 +325,9 @@ $(document).ready(function () {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>

55
docs/sqlScripts.html
View File

@ -368,12 +368,22 @@ div.tocify {
</a>
</li>
<li>
<a href="background.html">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-landmark"></span>
Background
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="background.html">Model Background</a>
</li>
<li>
<a href="vocabulary.html">How the Vocabulary is Built</a>
</li>
</ul>
</li>
<li>
<a href="dataModelConventions.html">
@ -391,6 +401,9 @@ div.tocify {
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="cdm30.html">CDM v3.0</a>
</li>
<li>
<a href="cdm531.html">CDM v5.3.1</a>
</li>
@ -531,7 +544,7 @@ div.tocify {
<h2><strong>Era Tables</strong></h2>
<div id="condition-eras" class="section level3">
<h3>Condition Eras</h3>
<p>This script will insert values into the CONDITION_ERA table given that the CONDITION_OCCURRENCE table is populated. It will string together condition records that have &lt;= 30 days between them into eras during which the Person is assumed to have the given condition.</p>
<p>This script will insert values into the CONDITION_ERA table given that the CONDITION_OCCURRENCE table is populated. It will string together condition records that have &lt;= 30 days between them into eras during which the Person is assumed to have the given condition. <strong>NOTE</strong> This query only works with 5.3 and below.</p>
<pre class="sql"><code>/****************************************************
OHDSI-SQL File Instructions
-----------------------------
@ -702,7 +715,7 @@ GROUP BY person_id
</div>
<div id="drug-eras" class="section level3">
<h3>Drug Eras</h3>
<p>If the DRUG_EXPOSURE table is populated this script will string together periods of time that a person is exposed to an active drug ingredient, allowing for 30 gaps in between. It will then insert the resulting era records into the DRUG_ERA table.</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 5.3 and below.</p>
<pre class="sql"><code>
/****************************************************
OHDSI-SQL File Instructions
@ -757,7 +770,7 @@ INTO #cteDrugTarget
FROM @TARGET_CDMV5_SCHEMA.DRUG_EXPOSURE d
INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
WHERE c.VOCABULARY_ID = &#39;RxNorm&#39;
WHERE c.DOMAIN_ID = &#39;Drug&#39;
AND c.CONCEPT_CLASS_ID = &#39;Ingredient&#39;;
/* / */
@ -873,6 +886,38 @@ GROUP BY person_id
</code></pre>
</div>
</div>
<div id="example-etl-script" class="section level2">
<h2><strong>Example ETL Script</strong></h2>
<div id="cdm_source-table" class="section level3">
<h3>CDM_SOURCE Table</h3>
<p>The script below is an example for how to fill in the CDM_SOURCE table. This table is required for the <a href="https://github.com/OHDSI/DataQualityDashboard">Data Quality Dashboard</a> package to run. This was taken from the <a href="https://github.com/OHDSI/ETL-Synthea">ETL-Synthea</a> package, a good example on how to write a complete extract-transform-load script from start to finish, including vocabulary import.</p>
<pre class="sql"><code>insert into @cdm_schema.cdm_source (
cdm_source_name,
cdm_source_abbreviation,
cdm_holder,
source_description,
source_documentation_reference,
cdm_etl_reference,
source_release_date,
cdm_release_date,
cdm_version,
vocabulary_version
)
select
&#39;Synthea synthetic health database&#39;,
&#39;Synthea&#39;,
&#39;OHDSI Community&#39;,
&#39;SyntheaTM is a Synthetic Patient Population Simulator. The goal is to output synthetic, realistic (but not real), patient data and associated health records in a variety of formats.&#39;,
&#39;https://synthetichealth.github.io/synthea/&#39;,
&#39;https://github.com/OHDSI/ETL-Synthea&#39;,
getdate(), -- NB: Set this value to the day the source data was pulled
getdate(),
&#39;v5.3&#39;,
vocabulary_version
from @cdm_schema.vocabulary
where vocabulary_id = &#39;None&#39;;</code></pre>
</div>
</div>
<div id="bonus-queries" class="section level2">
<h2><strong>Bonus Queries</strong></h2>
<div id="visit-concept-roll-up" class="section level3">

1242
docs/vocabulary.html Normal file
View File

File diff suppressed because it is too large Load Diff