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Merge pull request #473 from OHDSI/Jan2022_fixes 

Jan2022 fixes
This commit is contained in:
clairblacketer 2022-01-14 10:59:52 -05:00 committed by GitHub
parent 7e092bc44e f006431a5e
commit 5de46c92b6
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GPG Key ID: 4AEE18F83AFDEB23
72 changed files with 13962 additions and 2066 deletions
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2
R/listSupportedVersions.R
View File

@ -12,6 +12,6 @@ listSupportedVersions <- function() {
#' @export
listSupportedDialects <- function() {
supportedDialects <- c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")
supportedDialects <- c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark")
return(supportedDialects)
}

8
R/writeDDL.R
View File

@ -30,7 +30,7 @@
writeDdl <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
# argument checks
stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"))
stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark"))
stopifnot(cdmVersion %in% listSupportedVersions())
stopifnot(is.character(cdmDatabaseSchema))
@ -54,7 +54,7 @@ writeDdl <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema
writePrimaryKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
# argument checks
stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"))
stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark"))
stopifnot(cdmVersion %in% listSupportedVersions())
stopifnot(is.character(cdmDatabaseSchema))
@ -78,7 +78,7 @@ writePrimaryKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabas
writeForeignKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
# argument checks
stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"))
stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark"))
stopifnot(cdmVersion %in% listSupportedVersions())
stopifnot(is.character(cdmDatabaseSchema))
@ -102,7 +102,7 @@ writeForeignKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabas
writeIndex <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
# argument checks
stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"))
stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark"))
stopifnot(cdmVersion %in% listSupportedVersions())
stopifnot(is.character(cdmDatabaseSchema))

56
README.md
View File

@ -10,16 +10,15 @@ output:
# How to Use this Repository
If you are looking for the SQL DDLs and don't wish to generate them through R, they can be accessed [here](https://github.com/OHDSI/CommonDataModel/tree/v5.4.0/inst/ddl/5.4).
If you are looking for information on how to submit a bugfix, skip to the [next section](https://github.com/OHDSI/CommonDataModel#bug-fixesmodel-updates)
## Generating the DDLs
*By John and Sam Gresh*
If you prefer to generate the DDLs on your own without downloading them from the github tags, these instructions will guide you on how to do so.
This module will demonstrate two different ways the CDM R package can be used to create the CDM tables in your environment. First, it uses the `buildRelease` function to create the DDL files on your machine, intended for end users that wish to generate these scripts from R without the need to clone or download the source code from github. The SQL scripts that are created through this process are available as zip files as part of the [latest release](https://github.com/OHDSI/CommonDataModel/releases/tag/v5.4.0). They are also available on the master branch [here](https://github.com/OHDSI/CommonDataModel/tree/v5.4.0/inst/ddl/5.4).
### Introduction
This module will demonstrate how to individually create the DDL scripts for DDL, foreign keys, primary keys, and indexed for a single database instance at a time. This module is intended for end users that wish to generate these scripts from R without the need to clone or download the source code from github. The scripts that are created through this process are available as zip files here (TODO: NEED LINK).
Second, the script shows the `executeDdl` function that will connect up to your SQL client directly (assuming your dbms is one of the supported dialects) and instantiate the tables through R.
#### Dependencies and prerequisites
@ -27,27 +26,46 @@ This process required R-Studio to be installed as well as [DatabaseConnector](ht
#### Create DDL, Foreign Keys, Primary Keys, and Indexes from R
Launch R-Studio and create a new project: File -> New Project -> New Directory -> New Project
### First, install the package from GitHub
```
install.packages("devtools")
devtools::install_github("OHDSI/CommonDataModel")
```
### List the currently supported SQL dialects
```CommonDataModel::listSupportedDialects()```
After completing this step you should see something like the following:
### List the currently supported CDM versions
```CommonDataModel::listSupportedVersions()```
![](docs/images/rexample1.png)
For the next step, you can either open a new R script (File -> New File -> R Script), paste the text in the console, or open an R notebook (File -> New File -> New R Notebook). Whatever you choose, paste the following, replacing "output" with the name of the output file where you want the DDLs to appear and "YOUR_CDM_SCHEMA" with the name of your CDM schema. In this example we are generating the postgresql DDLs by specifying the dialect in the function calls. To determine which dialects are supported, run the `CommonDataModel::listSupportedDialects()` function.
```{r}
if (!require("devtools")) install.packages("devtools")
devtools::install_github("OHDSI/CommonDataModel", "v5.4")
CommonDataModel::buildRelease("postgresql", "5.4", "output", "YOUR_CDM_SCHEMA")
## 1. Use the `buildRelease` function
This function will generate the text files in the dialect you choose, putting the output files in the folder you specify.
```
CommonDataModel::buildRelease(cdmVersions = "5.4",
targetDialects = "postgresql",
outputfolder = "/pathToOutput")
```
![](docs/images/rexample2.png)
## 2. Use the `executeDdl` function
![](docs/images/rexample3.png)
If you have an empty schema ready to go, the package will connect and instantiate the tables for you. To start, you need to download DatabaseConnector in order to connect to your database.
```
devtools::install_github("DatabaseConnector")
cd <- DatabaseConnector::createConnectionDetails(dbms = "postgresql",
server = "localhost/ohdsi",
user = "postgres",
password = "postgres",
pathToDriver = "/pathToDriver"
)
CommonDataModel::executeDdl(connectionDetails = cd,
cdmVersion = "5.4",
cdmDatabaseSchema = "ohdsi_demo"
)
```
You will then see something like the above, with your output directory created and the DDLs available in the folder you specified.
## Bug Fixes/Model Updates

128
docs/background.html
View File

@ -11,15 +11,24 @@
<title>background.utf8</title>
<title>background.knit</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -590,7 +549,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -600,6 +559,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

126
docs/cdm30.html
View File

@ -13,13 +13,22 @@
<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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -554,7 +513,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -564,6 +523,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

138
docs/cdm53.html
View File

@ -13,13 +13,22 @@
<title>OMOP CDM v5.3</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -9249,7 +9208,7 @@ drug_era_start_date
The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure.
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -9275,7 +9234,7 @@ drug_era_end_date
The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules: For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information. For Procedure Drugs, usually the drug is administered on a single date (i.e., the administration date). A standard Persistence Window of 30 days (gap, slack) is permitted between two subsequent such extrapolated DRUG_EXPOSURE records to be considered to be merged into a single Drug Era.
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -9527,7 +9486,7 @@ The date the Person started on the specific dosage, with at least 31 days since
<td style="text-align:left;width: 4in; ">
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -9553,7 +9512,7 @@ dose_era_end_date
The date the Person was no longer exposed to the dosage of the specific drug ingredient. An era is ended if there are 31 days or more between dosage records.
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -9704,7 +9663,7 @@ The start date for the Condition Era constructed from the individual instances o
<td style="text-align:left;width: 4in; ">
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -9730,7 +9689,7 @@ The end date for the Condition Era constructed from the individual instances of
<td style="text-align:left;width: 4in; ">
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -12724,7 +12683,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -12734,6 +12693,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

126
docs/cdm531.html
View File

@ -13,13 +13,22 @@
<title>OMOP CDM v5.3.1</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -554,7 +513,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -564,6 +523,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

261
docs/cdm54.html
View File

@ -13,13 +13,22 @@
<title>OMOP CDM v5.4</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
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Conventions
@ -410,7 +369,7 @@ div.tocify {
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CDM Versions
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Proposals
@ -463,7 +422,7 @@ div.tocify {
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How to
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Support
@ -505,7 +464,7 @@ div.tocify {
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<p>Below is the specification document for the OMOP Common Data Model, v5.4. <strong>This is the latest version of the OMOP CDM.</strong> Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the <a href="https://forums.ohdsi.org/">forums</a> or the <a href="https://github.com/ohdsi/CommonDataModel/issues">github issue</a> page.</p>
<p>This is the specification document for the OMOP Common Data Model, v5.4. <strong>This is the latest version of the OMOP CDM.</strong> Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the <a href="https://forums.ohdsi.org/">forums</a> or the <a href="https://github.com/ohdsi/CommonDataModel/issues">github issue</a> page.</p>
<div id="current-support-for-cdm-v5.4" class="section level3">
<h3>Current Support for CDM v5.4</h3>
<p>The table below details which OHDSI tools support CDM v5.4. There are two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 that were not present in CDM v5.3. A green heart 💚 indicates that the support level for the listed tool is in place, has been tested, and released. A yellow heart 💛 indicates that the support level for the listed tool has been initiated but has not yet been tested and released. <br></p>
<table>
<colgroup>
<col width="25%" />
<col width="25%" />
<col width="25%" />
<col width="25%" />
</colgroup>
<thead>
<tr class="header">
<th><strong>Tool</strong></th>
<th><strong>Description</strong></th>
<th><strong>Legacy Support</strong></th>
<th><strong>Feature Support</strong></th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><strong>CDM R package</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/CommonDataModel/">https://github.com/OHDSI/CommonDataModel/</a>. It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables.</td>
<td>💚</td>
<td>💚</td>
</tr>
<tr class="even">
<td><strong>Data Quality Dashboard</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/DataQualityDashboard">https://github.com/OHDSI/DataQualityDashboard</a>. It runs a set of &gt; 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study.</td>
<td>💚</td>
<td>💛</td>
</tr>
<tr class="odd">
<td><strong>Achilles</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/Achilles">https://github.com/OHDSI/Achilles</a>, performing a set of broad database characterizations agains an OMOP CDM instance.</td>
<td>💚</td>
<td>💛</td>
</tr>
<tr class="even">
<td><strong>ARES</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/Ares">https://github.com/OHDSI/Ares</a> and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research.</td>
<td>💚</td>
<td>💛</td>
</tr>
<tr class="odd">
<td><strong>ATLAS</strong></td>
<td>ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. <a href="http://atlas-demo.ohdsi.org/">Demo</a></td>
<td>💚</td>
<td>💛</td>
</tr>
<tr class="even">
<td><strong>Rabbit-In-A-Hat</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/WhiteRabbit">https://github.com/OHDSI/WhiteRabbit</a> and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.</td>
<td>💚</td>
<td>💚</td>
</tr>
<tr class="odd">
<td><strong>Feature Extraction</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/FeatureExtraction">https://github.com/OHDSI/FeatureExtraction</a>. It is designed to generate features (covariates) for a cohort generated using the OMOP CDM.</td>
<td>💚</td>
<td>💚*</td>
</tr>
<tr class="even">
<td><strong>Cohort Diagnostics</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/CohortDiagnostics">https://github.com/OHDSI/CohortDiagnostics</a> and is used to critically evaluate cohort phenotypes.</td>
<td>💚</td>
<td>💛</td>
</tr>
</tbody>
</table>
<p><br> * The <strong>Feature Extraction</strong> package supports all relevant new features in CDM v5.4. For example, it was decided that, from a methodological perspective, the EPISODE and EPISODE_EVENT tables should not be included to define cohort covariates because the events that make up episodes are already pulled in as potential covariates.</p>
<p><br></p>
<p>Looking to send us a pull request for a bug fix? Please see the <a href="https://github.com/OHDSI/CommonDataModel#readme">readme</a> on the main github page.</p>
</div>
<div id="clinical-data-tables" class="section level2">
<h2><strong>Clinical Data Tables</strong></h2>
<div id="person" class="section level3 tabset tabset-pills">
@ -1222,7 +1253,7 @@ period_type_concept_id
This field can be used to determine the provenance of the Observation Period as in whether the period was determined from an insurance enrollment file, EHR healthcare encounters, or other sources.
</td>
<td style="text-align:left;width: 4in; ">
Choose the observation_period_type_concept_id that best represents how the period was determined. <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>.
Choose the observation_period_type_concept_id that best represents how the period was determined. <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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -1498,7 +1529,7 @@ visit_type_concept_id
Use this field to understand the provenance of the visit record, or where the record comes from.
</td>
<td style="text-align:left;width: 4in; ">
Populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim. <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>.
Populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim. <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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
Integer
@ -2008,7 +2039,7 @@ visit_detail_type_concept_id
Use this field to understand the provenance of the visit detail record, or where the record comes from.
</td>
<td style="text-align:left;width: 4in; ">
Populate this field based on the provenance of the visit detail record, as in whether it came from an EHR record or billing claim. <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>.
Populate this field based on the provenance of the visit detail record, as in whether it came from an EHR record or billing claim. <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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -2574,7 +2605,7 @@ condition_type_concept_id
This field can be used to determine the provenance of the Condition record, as in whether the condition was from an EHR system, insurance claim, registry, or other sources.
</td>
<td style="text-align:left;width: 4in; ">
Choose the CONDITION_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>.
Choose the CONDITION_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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -3085,7 +3116,7 @@ drug_type_concept_id
You can use the TYPE_CONCEPT_ID to delineate between prescriptions written vs. prescriptions dispensed vs. medication history vs. patient-reported exposure, etc.
</td>
<td style="text-align:left;width: 4in; ">
Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. <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>.
Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. <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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -3726,7 +3757,7 @@ procedure_type_concept_id
This field can be used to determine the provenance of the Procedure record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources.
</td>
<td style="text-align:left;width: 4in; ">
Choose the PROCEDURE_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. If a procedure is recorded as an EHR encounter, the PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter 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>.
Choose the PROCEDURE_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. If a procedure is recorded as an EHR encounter, the PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter 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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -4207,7 +4238,7 @@ device_type_concept_id
You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR.
</td>
<td style="text-align:left;width: 4in; ">
Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. <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>.
Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. <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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -4743,7 +4774,7 @@ measurement_type_concept_id
This field can be used to determine the provenance of the Measurement record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.
</td>
<td style="text-align:left;width: 4in; ">
Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. <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>.
Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. <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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -5162,7 +5193,7 @@ If the Measurement record is related to another record in the database, this fie
Put the primary key of the linked record, if applicable, here.
</td>
<td style="text-align:left;width: 1in; ">
bigint
integer
</td>
<td style="text-align:left;width: 1in; ">
No
@ -5393,7 +5424,7 @@ observation_type_concept_id
This field can be used to determine the provenance of the Observation record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.
</td>
<td style="text-align:left;width: 4in; ">
Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. <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>.
Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. <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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -5782,7 +5813,7 @@ If the Observation record is related to another record in the database, this fie
Put the primary key of the linked record, if applicable, here. See the <a href="https://ohdsi.github.io/CommonDataModel/cdm60.html#observation">ETL Conventions for the OBSERVATION</a> table for more details.
</td>
<td style="text-align:left;width: 1in; ">
bigint
integer
</td>
<td style="text-align:left;width: 1in; ">
No
@ -5953,7 +5984,7 @@ death_type_concept_id
This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.
</td>
<td style="text-align:left;width: 4in; ">
Use the type concept that be reflects the source of the death 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>.
Use the type concept that be reflects the source of the death 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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -6217,7 +6248,7 @@ note_type_concept_id
The provenance of the note. Most likely this will be EHR.
</td>
<td style="text-align:left;width: 4in; ">
Put the source system of the note, as in EHR record. <a href="https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&amp;domain=Type+Concept&amp;page=1&amp;pageSize=15&amp;query=">Accepted Concepts</a>.
Put the source system of the note, as in EHR record. <a href="https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&amp;domain=Type+Concept&amp;page=1&amp;pageSize=15&amp;query=">Accepted Concepts</a>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -6493,7 +6524,7 @@ If the Note record is related to another record in the database, this field is t
Put the primary key of the linked record, if applicable, here.
</td>
<td style="text-align:left;width: 1in; ">
bigint
integer
</td>
<td style="text-align:left;width: 1in; ">
No
@ -7071,7 +7102,7 @@ specimen_type_concept_id
<td style="text-align:left;width: 3in; ">
</td>
<td style="text-align:left;width: 4in; ">
Put the source of the specimen record, as in an EHR system. <a href="https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&amp;domain=Type+Concept&amp;page=1&amp;pageSize=15&amp;query=">Accepted Concepts</a>.
Put the source of the specimen record, as in an EHR system. <a href="https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&amp;domain=Type+Concept&amp;page=1&amp;pageSize=15&amp;query=">Accepted Concepts</a>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -7956,7 +7987,7 @@ care_site_id
<td style="text-align:left;width: 3in; ">
</td>
<td style="text-align:left;width: 4in; ">
Assign an id to each unique combination of location_id and place_of_service_source_value
Assign an ID to each combination of a location and nature of the site - the latter could be the Place of Service, name or another characteristic in your source data.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -9741,7 +9772,7 @@ drug_era_start_date
The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient, with at least 31 days since the previous exposure.
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -9767,7 +9798,7 @@ drug_era_end_date
The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules: For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information. For Procedure Drugs, usually the drug is administered on a single date (i.e., the administration date). A standard Persistence Window of 30 days (gap, slack) is permitted between two subsequent such extrapolated DRUG_EXPOSURE records to be considered to be merged into a single Drug Era.
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -10019,7 +10050,7 @@ The date the Person started on the specific dosage, with at least 31 days since
<td style="text-align:left;width: 4in; ">
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -10045,7 +10076,7 @@ dose_era_end_date
The date the Person was no longer exposed to the dosage of the specific drug ingredient. An era is ended if there are 31 days or more between dosage records.
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -10196,7 +10227,7 @@ The start date for the Condition Era constructed from the individual instances o
<td style="text-align:left;width: 4in; ">
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -10222,7 +10253,7 @@ The end date for the Condition Era constructed from the individual instances of
<td style="text-align:left;width: 4in; ">
</td>
<td style="text-align:left;width: 1in; ">
datetime
date
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -10316,7 +10347,7 @@ A unique identifier for each Episode.
<td style="text-align:left;width: 4in; ">
</td>
<td style="text-align:left;width: 1in; ">
bigint
integer
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -10342,7 +10373,7 @@ The PERSON_ID of the PERSON for whom the episode is recorded.
<td style="text-align:left;width: 4in; ">
</td>
<td style="text-align:left;width: 1in; ">
bigint
integer
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -10505,7 +10536,7 @@ Use this field to find the Episode that subsumes the given Episode record. This
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
integer
</td>
<td style="text-align:left;width: 1in; ">
No
@ -10585,7 +10616,7 @@ episode_type_concept_id
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>.
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>. A more detailed explanation of each Type Concept can be found on the <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary wiki</a>.
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -10715,7 +10746,7 @@ Use this field to link the EPISODE_EVENT record to its EPISODE.
Put the EPISODE_ID that subsumes the EPISODE_EVENT record here.
</td>
<td style="text-align:left;width: 1in; ">
bigint
integer
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -10743,7 +10774,7 @@ This field is the primary key of the linked record in the database. For example,
Put the primary key of the linked record here.
</td>
<td style="text-align:left;width: 1in; ">
bigint
integer
</td>
<td style="text-align:left;width: 1in; ">
Yes
@ -11342,6 +11373,7 @@ cdm_version_concept_id
The Concept Id representing the version of the CDM.
</td>
<td style="text-align:left;width: 4in; ">
You can find all concepts that represent the CDM versions using the query: SELECT * FROM CONCEPT WHERE VOCABULARY_ID = ‘CDM’ AND CONCEPT_CLASS = ‘CDM’
</td>
<td style="text-align:left;width: 1in; ">
integer
@ -11368,6 +11400,7 @@ vocabulary_version
<td style="text-align:left;width: 3in; ">
</td>
<td style="text-align:left;width: 4in; ">
You can find the version of your Vocabulary using the query: SELECT vocabulary_version from vocabulary where vocabulary_id = ‘None’
</td>
<td style="text-align:left;width: 1in; ">
varchar(20)
@ -13597,10 +13630,9 @@ Yes
No
</td>
<td style="text-align:left;width: 1in; ">
Yes
No
</td>
<td style="text-align:left;width: 1in; ">
COHORT
</td>
<td style="text-align:left;width: 1in; ">
</td>
@ -13797,7 +13829,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -13807,6 +13839,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

126
docs/cdm54Changes.html
View File

@ -13,13 +13,22 @@
<title>Changes by Table</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -891,7 +850,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -901,6 +860,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

126
docs/cdm60.html
View File

@ -13,13 +13,22 @@
<title>OMOP CDM v6.0</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -13601,7 +13560,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -13611,6 +13570,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

128
docs/cdmPrivacy.html
View File

@ -13,13 +13,22 @@
<title>Preserving Privacy in an OMOP CDM Implementation</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,11 +473,11 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
<h1 class="title toc-ignore">Preserving Privacy in an OMOP CDM Implementation</h1>
<h1 class="title toc-ignore"><strong>Preserving Privacy in an OMOP CDM Implementation</strong></h1>
</div>
@ -667,7 +626,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -677,6 +636,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

128
docs/cdmRefreshProcess.html
View File

@ -11,15 +11,24 @@
<title>cdmRefreshProcess.utf8</title>
<title>cdmRefreshProcess.knit</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -596,7 +555,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -606,6 +565,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

126
docs/contribute.html
View File

@ -13,13 +13,22 @@
<title>Ask A Question</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -565,7 +524,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -575,6 +534,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

128
docs/dataModelConventions.html
View File

@ -11,15 +11,24 @@
<title>dataModelConventions.utf8</title>
<title>dataModelConventions.knit</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -886,7 +845,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -896,6 +855,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

126
docs/download.html
View File

@ -13,13 +13,22 @@
<title>Download</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -555,7 +514,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -565,6 +524,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

123
docs/drug_dose.html
View File

@ -13,15 +13,24 @@
<meta name="date" content="2020-10-06" />
<title>drug_dose.utf8</title>
<title>drug_dose.knit</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
@ -39,11 +48,6 @@
</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: []});
@ -56,32 +60,6 @@ if (window.hljs) {
<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" />
@ -94,10 +72,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -113,40 +87,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -174,7 +121,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -186,7 +133,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -197,10 +144,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -212,7 +172,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -290,13 +249,13 @@ $(document).ready(function () {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -316,7 +275,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -336,7 +295,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -367,7 +326,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -389,7 +348,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -409,7 +368,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -431,7 +390,7 @@ $(document).ready(function () {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -440,7 +399,7 @@ $(document).ready(function () {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -482,7 +441,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>

123
docs/ehrObsPeriods.html
View File

@ -13,13 +13,22 @@
<title>Observation Period Considerations for EHR Data</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
@ -37,11 +46,6 @@
</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: []});
@ -54,32 +58,6 @@ if (window.hljs) {
<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" />
@ -92,10 +70,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -111,40 +85,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -172,7 +119,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
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@ -334,7 +293,7 @@ $(document).ready(function () {
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CDM Versions
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<li>
<a href="https://github.com/OHDSI/CommonDataModel">
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</a>
</li>
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</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
<h1 class="title toc-ignore">Observation Period Considerations for EHR Data</h1>
<h1 class="title toc-ignore"><strong>Observation Period Considerations for EHR Data</strong></h1>
</div>
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<title>OMOP CDM Frequently Asked Questions</title>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -334,7 +293,7 @@ $(document).ready(function () {
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<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -365,7 +324,7 @@ $(document).ready(function () {
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<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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Proposals
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How to
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -429,7 +388,7 @@ $(document).ready(function () {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -438,7 +397,7 @@ $(document).ready(function () {
</div><!--/.container -->
</div><!--/.navbar -->
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});
</script>

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@ -11,15 +11,24 @@
<title>index.utf8</title>
<title>index.knit</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>
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@ -37,11 +46,6 @@
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background-color: white;
}
</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
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}
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color: inherit;
background-color: rgba(0, 0, 0, 0.04);
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max-width:100%;
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summary {
display: list-item;
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pre code {
padding: 0;
}
</style>
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body {
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}
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@ -184,7 +131,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -195,10 +142,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
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var mt = "margin-top: -" + navHeight + "px; ";
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background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -288,13 +247,13 @@ $(document).ready(function () {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -314,7 +273,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -334,7 +293,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -365,7 +324,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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How to
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<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -429,7 +388,7 @@ $(document).ready(function () {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -438,7 +397,7 @@ $(document).ready(function () {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -455,10 +414,82 @@ $(document).ready(function () {
<h2>Current CDM Version</h2>
<p>The current CDM version is <a href="http://ohdsi.github.io/CommonDataModel/cdm54.html">CDM v5.4</a>, depicted below. This CDM version was developed over the course of a year by considering requests that were sent via our <a href="https://github.com/OHDSI/CommonDataModel/issues">issues page</a>. The list of proposed changes was then shared with the community in multiple ways: through discussions at the weekly OHDSI Community calls, discussions with the OHDSI Steering Committee, and discussions with all potentially affected workgroups. The <a href="http://ohdsi.github.io/CommonDataModel/cdm54Changes.html">final changes</a> were then delivered to the Community through a new R package designed to dynamically generate the DDLs and documentation for all supported SQL dialects.</p>
<ul>
<li><a href="https://github.com/OHDSI/CommonDataModel/tree/v5.4.0">Link to DDLs for CDM v5.4</a></li>
<li><a href="https://github.com/OHDSI/CommonDataModel/tree/v5.4.0/inst/ddl/5.4">Link to DDLs for CDM v5.4</a></li>
<li><a href="https://github.com/OHDSI/CommonDataModel/tree/master#readme">Link to ReadMe for instructions on how to use the R package</a></li>
</ul>
<p><img src="images/cdm54.png" /> <br></p>
<div id="current-support-for-cdm-v5.4" class="section level3">
<h3>Current Support for CDM v5.4</h3>
<p>The table below details which OHDSI tools support CDM v5.4. There are two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 that were not present in CDM v5.3. A green heart 💚 indicates that the support level for the listed tool is in place, has been tested, and released. A yellow heart 💛 indicates that the support level for the listed tool has been initiated but has not yet been tested and released. <br></p>
<table>
<colgroup>
<col width="25%" />
<col width="25%" />
<col width="25%" />
<col width="25%" />
</colgroup>
<thead>
<tr class="header">
<th><strong>Tool</strong></th>
<th><strong>Description</strong></th>
<th><strong>Legacy Support</strong></th>
<th><strong>Feature Support</strong></th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><strong>CDM R package</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/CommonDataModel/">https://github.com/OHDSI/CommonDataModel/</a>. It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables.</td>
<td>💚</td>
<td>💚</td>
</tr>
<tr class="even">
<td><strong>Data Quality Dashboard</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/DataQualityDashboard">https://github.com/OHDSI/DataQualityDashboard</a>. It runs a set of &gt; 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study.</td>
<td>💚</td>
<td>💛</td>
</tr>
<tr class="odd">
<td><strong>Achilles</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/Achilles">https://github.com/OHDSI/Achilles</a>, performing a set of broad database characterizations agains an OMOP CDM instance.</td>
<td>💚</td>
<td>💛</td>
</tr>
<tr class="even">
<td><strong>ARES</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/Ares">https://github.com/OHDSI/Ares</a> and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research.</td>
<td>💚</td>
<td>💛</td>
</tr>
<tr class="odd">
<td><strong>ATLAS</strong></td>
<td>ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. <a href="http://atlas-demo.ohdsi.org/">Demo</a></td>
<td>💚</td>
<td>💛</td>
</tr>
<tr class="even">
<td><strong>Rabbit-In-A-Hat</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/WhiteRabbit">https://github.com/OHDSI/WhiteRabbit</a> and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.</td>
<td>💚</td>
<td>💚</td>
</tr>
<tr class="odd">
<td><strong>Feature Extraction</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/FeatureExtraction">https://github.com/OHDSI/FeatureExtraction</a>. It is designed to generate features (covariates) for a cohort generated using the OMOP CDM.</td>
<td>💚</td>
<td>💚*</td>
</tr>
<tr class="even">
<td><strong>Cohort Diagnostics</strong></td>
<td>This package can be downloaded from <a href="https://github.com/OHDSI/CohortDiagnostics">https://github.com/OHDSI/CohortDiagnostics</a> and is used to critically evaluate cohort phenotypes.</td>
<td>💚</td>
<td>💛</td>
</tr>
</tbody>
</table>
<p><br> * The <strong>Feature Extraction</strong> package supports all relevant new features in CDM v5.4. For example, it was decided that, from a methodological perspective, the EPISODE and EPISODE_EVENT tables should not be included to define cohort covariates because the events that make up episodes are already pulled in as potential covariates.</p>
<p><br></p>
</div>
</div>
<div id="the-cdm-working-group" class="section level2">
<h2>The CDM Working Group</h2>
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121
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</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -409,7 +368,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -431,7 +390,7 @@ $(document).ready(function () {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -440,7 +399,7 @@ $(document).ready(function () {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -481,7 +440,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>

121
docs/reviewProposals.html
View File

@ -13,13 +13,22 @@
<title>CDM Proposals Under Review</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
@ -37,11 +46,6 @@
</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: []});
@ -54,32 +58,6 @@ if (window.hljs) {
<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" />
@ -92,10 +70,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -111,40 +85,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -172,7 +119,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -184,7 +131,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -195,10 +142,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -210,7 +170,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -288,13 +247,13 @@ $(document).ready(function () {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -314,7 +273,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -334,7 +293,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -365,7 +324,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -387,7 +346,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -407,7 +366,7 @@ $(document).ready(function () {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -429,7 +388,7 @@ $(document).ready(function () {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -438,7 +397,7 @@ $(document).ready(function () {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -476,7 +435,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>

0
docs/site_libs/header-attrs-2.6/header-attrs.js → docs/site_libs/header-attrs-2.11/header-attrs.js
View File

5
docs/site_libs/jquery-1.11.3/jquery.min.js vendored
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10881
docs/site_libs/jquery-3.6.0/jquery-3.6.0.js vendored Normal file
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2
docs/site_libs/jquery-3.6.0/jquery-3.6.0.min.js vendored Normal file
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1
docs/site_libs/jquery-3.6.0/jquery-3.6.0.min.map Normal file
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19
docs/site_libs/navigation-1.1/codefolding.js
View File

@ -23,7 +23,6 @@ window.initializeCodeFolding = function(show) {
// create a collapsable div to wrap the code in
var div = $('<div class="collapse r-code-collapse"></div>');
var showThis = (show || $(this).hasClass('fold-show')) && !$(this).hasClass('fold-hide');
if (showThis) div.addClass('in');
var id = 'rcode-643E0F36' + currentIndex++;
div.attr('id', id);
$(this).before(div);
@ -31,7 +30,7 @@ window.initializeCodeFolding = function(show) {
// add a show code button right above
var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Code') + '</span>');
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs code-folding-btn pull-right"></button>');
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm code-folding-btn pull-right float-right"></button>');
showCodeButton.append(showCodeText);
showCodeButton
.attr('data-toggle', 'collapse')
@ -47,13 +46,27 @@ window.initializeCodeFolding = function(show) {
div.before(buttonRow);
// show the div if necessary
if (showThis) div.collapse('show');
// update state of button on show/hide
div.on('hidden.bs.collapse', function () {
// * Change text
// * add a class for intermediate states styling
div.on('hide.bs.collapse', function () {
showCodeText.text('Code');
showCodeButton.addClass('btn-collapsing');
});
div.on('hidden.bs.collapse', function () {
showCodeButton.removeClass('btn-collapsing');
});
div.on('show.bs.collapse', function () {
showCodeText.text('Hide');
showCodeButton.addClass('btn-expanding');
});
div.on('shown.bs.collapse', function () {
showCodeButton.removeClass('btn-expanding');
});
});
}

2
docs/site_libs/tocify-1.9.1/jquery.tocify.js
View File

@ -176,7 +176,7 @@
self._setEventHandlers();
// Binding to the Window load event to make sure the correct scrollTop is calculated
$(window).load(function() {
$(window).on("load", function() {
// Sets the active TOC item
self._setActiveElement(true);

131
docs/sqlScripts.html
View File

@ -11,15 +11,24 @@
<title>sqlScripts.utf8</title>
<title>sqlScripts.knit</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -795,7 +754,8 @@ FROM @TARGET_CDMV5_SCHEMA.DRUG_EXPOSURE d
INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
WHERE c.DOMAIN_ID = &#39;Drug&#39;
AND c.CONCEPT_CLASS_ID = &#39;Ingredient&#39;;
AND c.CONCEPT_CLASS_ID = &#39;Ingredient&#39;
AND c.STANDARD_CONCEPT = &#39;S&#39;;
/* / */
@ -988,7 +948,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -998,6 +958,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

126
docs/vocabulary.html
View File

@ -13,13 +13,22 @@
<title>How the Vocabulary is Built</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>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
@ -40,11 +49,6 @@
</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: []});
@ -57,32 +61,6 @@ if (window.hljs) {
<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" />
@ -95,10 +73,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
@ -114,40 +88,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
@ -175,7 +122,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
@ -187,7 +134,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
@ -198,10 +145,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
@ -213,7 +173,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
@ -339,7 +298,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
@ -364,13 +323,13 @@ div.tocify {
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home"></span>
<span class="fa 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>
<span class="fa fa-landmark"></span>
Background
@ -390,7 +349,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-list-alt"></span>
<span class="fa fa-list-alt"></span>
Conventions
@ -410,7 +369,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-history"></span>
<span class="fa fa-history"></span>
CDM Versions
@ -441,7 +400,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-plus-square"></span>
<span class="fa fa-plus-square"></span>
Proposals
@ -463,7 +422,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question"></span>
<span class="fa fa-question"></span>
How to
@ -483,7 +442,7 @@ div.tocify {
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-life-ring"></span>
<span class="fa fa-life-ring"></span>
Support
@ -505,7 +464,7 @@ div.tocify {
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/OHDSI/CommonDataModel">
<span class="fas fa-github"></span>
<span class="fa fa-github"></span>
</a>
</li>
@ -514,7 +473,7 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
@ -1220,7 +1179,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
@ -1230,6 +1189,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')

12
extras/codeToRun.R
View File

@ -1,13 +1,13 @@
# This script is meant to create the OMOP Common Data Model DDLs for each dialect as well as the pdf of the documentation.
# For a given cdmVersion, create all ddl sql files for every sql dialect
# Results are written to ddl/cdm_version/dialect.
cdmVersion <- "5.3"
# Results are written to inst/ddl/cdm_version/dialect.
cdmVersion <- "5.4"
supportedVersions <- listSupportedVersions()
for (cdmVersion in supportedVersions) {
for (targetDialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) {
for (targetDialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark")) {
writeDdl(targetDialect = targetDialect,
cdmVersion = cdmVersion)
@ -22,10 +22,14 @@ for (cdmVersion in supportedVersions) {
}
}
CommonDataModel::buildRelease("5.4")
#############
# Zipping release
# All dialects
buildReleaseZip(cdmVersion="5.3", outputfolder="output")
buildReleaseZip(cdmVersion="5.4", outputfolder="output")
buildReleaseZip()
# One dialect
buildReleaseZip(cdmVersion="5.4", targetDialect="postgresql", outputfolder="output")

48
inst/csv/OMOP_CDMv5.4_Field_Level.csv
View File

@ -21,7 +21,7 @@ OBSERVATION_PERIOD,observation_period_id,Yes,integer,A Person can have multiple
OBSERVATION_PERIOD,person_id,Yes,integer,The Person ID of the PERSON record for which the Observation Period is recorded.,,No,Yes,PERSON,PERSON_ID,,,
OBSERVATION_PERIOD,observation_period_start_date,Yes,date,Use this date to determine the start date of the Observation Period.,"It is often the case that the idea of Observation Periods does not exist in source data. In those cases, the observation_period_start_date can be inferred as the earliest Event date available for the Person. In insurance claim data, the Observation Period can be considered as the time period the Person is enrolled with a payer. If a Person switches plans but stays with the same payer, and therefore capturing of data continues, that change would be captured in [PAYER_PLAN_PERIOD](https://ohdsi.github.io/CommonDataModel/cdm531.html#payer_plan_period).",No,No,,,,,
OBSERVATION_PERIOD,observation_period_end_date,Yes,date,Use this date to determine the end date of the period for which we can assume that all events for a Person are recorded.,"It is often the case that the idea of Observation Periods does not exist in source data. In those cases, the observation_period_end_date can be inferred as the last Event date available for the Person. In insurance claim data, the Observation Period can be considered as the time period the Person is enrolled with a payer.",No,No,,,,,
OBSERVATION_PERIOD,period_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Observation Period as in whether the period was determined from an insurance enrollment file, EHR healthcare encounters, or other sources.",Choose the observation_period_type_concept_id that best represents how the period was determined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
OBSERVATION_PERIOD,period_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Observation Period as in whether the period was determined from an insurance enrollment file, EHR healthcare encounters, or other sources.",Choose the observation_period_type_concept_id that best represents how the period was determined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
VISIT_OCCURRENCE,visit_occurrence_id,Yes,integer,Use this to identify unique interactions between a person and the health care system. This identifier links across the other CDM event tables to associate events with a visit.,This should be populated by creating a unique identifier for each unique interaction between a person and the healthcare system where the person receives a medical good or service over a span of time.,Yes,No,,,,,
VISIT_OCCURRENCE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
VISIT_OCCURRENCE,visit_concept_id,Yes,integer,"This field contains a concept id representing the kind of visit, like inpatient or outpatient. All concepts in this field should be standard and belong to the Visit domain.","Populate this field based on the kind of visit that took place for the person. For example this could be ""Inpatient Visit"", ""Outpatient Visit"", ""Ambulatory Visit"", etc. This table will contain standard concepts in the Visit domain. These concepts are arranged in a hierarchical structure to facilitate cohort definitions by rolling up to generally familiar Visits adopted in most healthcare systems worldwide. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
@ -35,7 +35,7 @@ VISIT_OCCURRENCE,visit_end_date,Yes,date,"For inpatient visits the end date is t
For Inpatient Visits ongoing at the date of ETL, put date of processing the data into visit_end_datetime and visit_type_concept_id with 32220 ""Still patient"" to identify the visit as incomplete.
- All other Visits: visit_end_datetime = visit_start_datetime. If this is a one-day visit the end date should match the start date.",No,No,,,,,
VISIT_OCCURRENCE,visit_end_datetime,No,datetime,"If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_datetime, then set the visit_end_datetime to the datetime of the data pull.","If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,,,,,
VISIT_OCCURRENCE,visit_type_concept_id,Yes,Integer,"Use this field to understand the provenance of the visit record, or where the record comes from.","Populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
VISIT_OCCURRENCE,visit_type_concept_id,Yes,Integer,"Use this field to understand the provenance of the visit record, or where the record comes from.","Populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
VISIT_OCCURRENCE,provider_id,No,integer,"There will only be one provider per visit record and the ETL document should clearly state how they were chosen (attending, admitting, etc.). If there are multiple providers associated with a visit in the source, this can be reflected in the event tables (CONDITION_OCCURRENCE, PROCEDURE_OCCURRENCE, etc.) or in the VISIT_DETAIL table.","If there are multiple providers associated with a visit, you will need to choose which one to put here. The additional providers can be stored in the [VISIT_DETAIL](https://ohdsi.github.io/CommonDataModel/cdm531.html#visit_detail) table.",No,Yes,PROVIDER,PROVIDER_ID,,,
VISIT_OCCURRENCE,care_site_id,No,integer,This field provides information about the Care Site where the Visit took place.,There should only be one Care Site associated with a Visit.,No,Yes,CARE_SITE,CARE_SITE_ID,,,
VISIT_OCCURRENCE,visit_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the kind of visit that took place (inpatient, outpatient, emergency, etc.)","If there is information about the kind of visit in the source data that value should be stored here. If a visit is an amalgamation of visits from the source then use a hierarchy to choose the visit source value, such as IP -> ER-> OP. This should line up with the logic chosen to determine how visits are created.",No,No,,,,,
@ -58,7 +58,7 @@ VISIT_DETAIL,visit_detail_end_date,Yes,date,"This the end date of the patient-pr
For Inpatient Visit Details ongoing at the date of ETL, put date of processing the data into visit_detai_end_datetime and visit_detail_type_concept_id with 32220 ""Still patient"" to identify the visit as incomplete.
All other Visits Details: visit_detail_end_datetime = visit_detail_start_datetime. ",No,No,,,,,
VISIT_DETAIL,visit_detail_end_datetime,No,datetime,"If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_datetime, then set the visit_end_datetime to the datetime of the data pull.","If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,,,,,
VISIT_DETAIL,visit_detail_type_concept_id,Yes,integer,"Use this field to understand the provenance of the visit detail record, or where the record comes from.","Populate this field based on the provenance of the visit detail record, as in whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
VISIT_DETAIL,visit_detail_type_concept_id,Yes,integer,"Use this field to understand the provenance of the visit detail record, or where the record comes from.","Populate this field based on the provenance of the visit detail record, as in whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
VISIT_DETAIL,provider_id,No,integer,"There will only be one provider per **visit** record and the ETL document should clearly state how they were chosen (attending, admitting, etc.). This is a typical reason for leveraging the VISIT_DETAIL table as even though each VISIT_DETAIL record can only have one provider, there is no limit to the number of VISIT_DETAIL records that can be associated to a VISIT_OCCURRENCE record.",The additional providers associated to a Visit can be stored in this table where each VISIT_DETAIL record represents a different provider.,No,Yes,PROVIDER,PROVIDER_ID,,,
VISIT_DETAIL,care_site_id,No,integer,This field provides information about the Care Site where the Visit Detail took place.,There should only be one Care Site associated with a Visit Detail.,No,Yes,CARE_SITE,CARE_SITE_ID,,,
VISIT_DETAIL,visit_detail_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the kind of visit detail that took place (inpatient, outpatient, emergency, etc.)","If there is information about the kind of visit detail in the source data that value should be stored here. If a visit is an amalgamation of visits from the source then use a hierarchy to choose the VISIT_DETAIL_SOURCE_VALUE, such as IP -> ER-> OP. This should line up with the logic chosen to determine how visits are created.",No,No,,,,,
@ -77,7 +77,7 @@ CONDITION_OCCURRENCE,condition_start_date,Yes,date,Use this date to determine th
CONDITION_OCCURRENCE,condition_start_datetime,No,datetime,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,,,,,
CONDITION_OCCURRENCE,condition_end_date,No,date,Use this date to determine the end date of the condition,"Most often data sources do not have the idea of a start date for a condition. Rather, if a source only has one date associated with a condition record it is acceptable to use that date for both the CONDITION_START_DATE and the CONDITION_END_DATE.",No,No,,,,,
CONDITION_OCCURRENCE,condition_end_datetime,No,datetime,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,,,,,
CONDITION_OCCURRENCE,condition_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Condition record, as in whether the condition was from an EHR system, insurance claim, registry, or other sources.",Choose the CONDITION_TYPE_CONCEPT_ID that best represents the provenance of the record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
CONDITION_OCCURRENCE,condition_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Condition record, as in whether the condition was from an EHR system, insurance claim, registry, or other sources.",Choose the CONDITION_TYPE_CONCEPT_ID that best represents the provenance of the record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
CONDITION_OCCURRENCE,condition_status_concept_id,No,integer,"This concept represents the point during the visit the diagnosis was given (admitting diagnosis, final diagnosis), whether the diagnosis was determined due to laboratory findings, if the diagnosis was exclusionary, or if it was a preliminary diagnosis, among others. ","Choose the Concept in the Condition Status domain that best represents the point during the visit when the diagnosis was given. These can include admitting diagnosis, principal diagnosis, and secondary diagnosis. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Condition Status,,
CONDITION_OCCURRENCE,stop_reason,No,varchar(20),The Stop Reason indicates why a Condition is no longer valid with respect to the purpose within the source data. Note that a Stop Reason does not necessarily imply that the condition is no longer occurring.,This information is often not populated in source data and it is a valid etl choice to leave it blank if the information does not exist.,No,No,,,,,
CONDITION_OCCURRENCE,provider_id,No,integer,"The provider associated with condition record, e.g. the provider who made the diagnosis or the provider who recorded the symptom.","The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record, for example the admitting vs attending physician on an EHR record.",No,Yes,PROVIDER,PROVIDER_ID,,,
@ -94,7 +94,7 @@ DRUG_EXPOSURE,drug_exposure_start_datetime,No,datetime,,"This is not required, t
DRUG_EXPOSURE,drug_exposure_end_date,Yes,date,The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient.,"If this information is not explicitly available in the data, infer the end date using the following methods:<br><br> 1. Start first with duration or days supply using the calculation drug start date + days supply -1 day. 2. Use quantity divided by daily dose that you may obtain from the sig or a source field (or assumed daily dose of 1) for solid, indivisibile, drug products. If quantity represents ingredient amount, quantity divided by daily dose * concentration (from drug_strength) drug concept id tells you the dose form. 3. If it is an administration record, set drug end date equal to drug start date. If the record is a written prescription then set end date to start date + 29. If the record is a mail-order prescription set end date to start date + 89. The end date must be equal to or greater than the start date. Ibuprofen 20mg/mL oral solution concept tells us this is oral solution. Calculate duration as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL) 200*5/20 = 50 days. [Examples by dose form](https://ohdsi.github.io/CommonDataModel/drug_dose.html)",No,No,,,,,
DRUG_EXPOSURE,drug_exposure_end_datetime,No,datetime,,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,,,,,
DRUG_EXPOSURE,verbatim_end_date,No,date,"This is the end date of the drug exposure as it appears in the source data, if it is given",Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable.,No,No,,,,,
DRUG_EXPOSURE,drug_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to delineate between prescriptions written vs. prescriptions dispensed vs. medication history vs. patient-reported exposure, etc.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
DRUG_EXPOSURE,drug_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to delineate between prescriptions written vs. prescriptions dispensed vs. medication history vs. patient-reported exposure, etc.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
DRUG_EXPOSURE,stop_reason,No,varchar(20),"The reason a person stopped a medication as it is represented in the source. Reasons include regimen completed, changed, removed, etc. This field will be retired in v6.0.",This information is often not populated in source data and it is a valid etl choice to leave it blank if the information does not exist.,No,No,,,,,
DRUG_EXPOSURE,refills,No,integer,This is only filled in when the record is coming from a prescription written this field is meant to represent intended refills at time of the prescription.,,No,No,,,,,
DRUG_EXPOSURE,quantity,No,float,,"To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is 'Has dose form'. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160.
@ -118,7 +118,7 @@ PROCEDURE_OCCURRENCE,procedure_date,Yes,date,Use this date to determine the date
PROCEDURE_OCCURRENCE,procedure_datetime,No,datetime,,"If the procedure has a start time in the native date, use this field to house that information. This will be renamed in a future version to **PROCEDURE_START_DATETIME**.",No,No,,,,,
PROCEDURE_OCCURRENCE,procedure_end_date,No,date,Use this field to house the date that the procedure ended. ,This is meant to be the end date of the procedure. It is not required and for most cases will be the same as the PROCEDURE_START_DATE.,No,No,,,,,
PROCEDURE_OCCURRENCE,procedure_end_datetime,No,datetime,Use this field to house the datetime that the procedure ended. ,This is meant to house the end datetime of the procedure and will most often be used in conjunction with the procedure_start_datetime to determine the length of the procedure.,No,No,,,,,
PROCEDURE_OCCURRENCE,procedure_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Procedure record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources.","Choose the PROCEDURE_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. If a procedure is recorded as an EHR encounter, the PROCEDURE_TYPE_CONCEPT would be 'EHR encounter record'. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
PROCEDURE_OCCURRENCE,procedure_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Procedure record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources.","Choose the PROCEDURE_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. If a procedure is recorded as an EHR encounter, the PROCEDURE_TYPE_CONCEPT would be 'EHR encounter record'. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
PROCEDURE_OCCURRENCE,modifier_concept_id,No,integer,The modifiers are intended to give additional information about the procedure but as of now the vocabulary is under review.,"It is up to the ETL to choose how to map modifiers if they exist in source data. These concepts are typically distinguished by 'Modifier' concept classes (e.g., 'CPT4 Modifier' as part of the 'CPT4' vocabulary). If there is more than one modifier on a record, one should be chosen that pertains to the procedure rather than provider. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?conceptClass=CPT4+Modifier&conceptClass=HCPCS+Modifier&vocabulary=CPT4&vocabulary=HCPCS&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,,
PROCEDURE_OCCURRENCE,quantity,No,integer,"If the quantity value is omitted, a single procedure is assumed.","If a Procedure has a quantity of '0' in the source, this should default to '1' in the ETL. If there is a record in the source it can be assumed the exposure occurred at least once",No,No,,,,,
PROCEDURE_OCCURRENCE,provider_id,No,integer,"The provider associated with the procedure record, e.g. the provider who performed the Procedure.","The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record, for example the admitting vs attending physician on an EHR record.",No,Yes,PROVIDER,PROVIDER_ID,,,
@ -134,7 +134,7 @@ DEVICE_EXPOSURE,device_exposure_start_date,Yes,date,Use this date to determine t
DEVICE_EXPOSURE,device_exposure_start_datetime,No,datetime,,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,,,,,
DEVICE_EXPOSURE,device_exposure_end_date,No,date,"The DEVICE_EXPOSURE_END_DATE denotes the day the device exposure ended for the patient, if given.",Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable.,No,No,,,,,
DEVICE_EXPOSURE,device_exposure_end_datetime,No,datetime,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,,,,,
DEVICE_EXPOSURE,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR. ","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
DEVICE_EXPOSURE,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR. ","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
DEVICE_EXPOSURE,unique_device_id,No,varchar(255),"This is the Unique Device Identification (UDI-DI) number for devices regulated by the FDA, if given. ","For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field.",No,No,,,,,
DEVICE_EXPOSURE,production_id,No,varchar(255),This is the Production Identifier (UDI-PI) portion of the Unique Device Identification.,,No,No,,,,,
DEVICE_EXPOSURE,quantity,No,integer,,,No,No,,,,,
@ -152,7 +152,7 @@ MEASUREMENT,measurement_concept_id,Yes,integer,"The MEASUREMENT_CONCEPT_ID field
MEASUREMENT,measurement_date,Yes,date,Use this date to determine the date of the measurement.,"If there are multiple dates in the source data associated with a record such as order_date, draw_date, and result_date, choose the one that is closest to the date the sample was drawn from the patient.",No,No,,,,,
MEASUREMENT,measurement_datetime,No,datetime,,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,,,,,
MEASUREMENT,measurement_time,No,varchar(10),,This is present for backwards compatibility and will be deprecated in an upcoming version.,No,No,,,,,
MEASUREMENT,measurement_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Measurement record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.","Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
MEASUREMENT,measurement_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Measurement record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.","Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
MEASUREMENT,operator_concept_id,No,integer,"The meaning of Concept [4172703](https://athena.ohdsi.org/search-terms/terms/4172703) for '=' is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, it's important when devising analyses to not to forget testing for the content of this field for values different from =.","Operators are <, <=, =, >=, > and these concepts belong to the 'Meas Value Operator' domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,,
MEASUREMENT,value_as_number,No,float,"This is the numerical value of the Result of the Measurement, if available. Note that measurements such as blood pressures will be split into their component parts i.e. one record for systolic, one record for diastolic.","If there is a negative value coming from the source, set the VALUE_AS_NUMBER to NULL, with the exception of the following Measurements (listed as LOINC codes):<br>- [1925-7](https://athena.ohdsi.org/search-terms/terms/3003396) Base excess in Arterial blood by calculation - [1927-3](https://athena.ohdsi.org/search-terms/terms/3002032) Base excess in Venous blood by calculation - [8632-2](https://athena.ohdsi.org/search-terms/terms/3006277) QRS-Axis - [11555-0](https://athena.ohdsi.org/search-terms/terms/3012501) Base excess in Blood by calculation - [1926-5](https://athena.ohdsi.org/search-terms/terms/3003129) Base excess in Capillary blood by calculation - [28638-5](https://athena.ohdsi.org/search-terms/terms/3004959) Base excess in Arterial cord blood by calculation [28639-3](https://athena.ohdsi.org/search-terms/terms/3007435) Base excess in Venous cord blood by calculation",No,No,,,,,
MEASUREMENT,value_as_concept_id,No,integer,If the raw data gives a categorial result for measurements those values are captured and mapped to standard concepts in the 'Meas Value' domain.,"If the raw data provides categorial results as well as continuous results for measurements, it is a valid ETL choice to preserve both values. The continuous value should go in the VALUE_AS_NUMBER field and the categorical value should be mapped to a standard concept in the 'Meas Value' domain and put in the VALUE_AS_CONCEPT_ID field. This is also the destination for the 'Maps to value' relationship.",No,Yes,CONCEPT,CONCEPT_ID,,,
@ -167,14 +167,14 @@ MEASUREMENT,measurement_source_concept_id,No,integer,"This is the concept repres
MEASUREMENT,unit_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the unit of the Measurement that occurred. ,This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,No,,,,,
MEASUREMENT,unit_source_concept_id,No,integer,"""This is the concept representing the UNIT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Measurement necessary for a given analytic use case. Consider using UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.""",If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,,
MEASUREMENT,value_source_value,No,varchar(50),This field houses the verbatim result value of the Measurement from the source data . ,"If both a continuous and categorical result are given in the source data such that both VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are both included, store the verbatim value that was mapped to VALUE_AS_CONCEPT_ID here.",No,No,,,,,
MEASUREMENT,measurement_event_id,No,bigint,"If the Measurement record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here.",No,No,,,,,
MEASUREMENT,measurement_event_id,No,integer,"If the Measurement record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here.",No,No,,,,,
MEASUREMENT,meas_event_field_concept_id,No,integer,"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. ",Put the CONCEPT_ID that identifies which table and field the MEASUREMENT_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,,,
OBSERVATION,observation_id,Yes,integer,The unique key given to an Observation record for a Person. Refer to the ETL for how duplicate Observations during the same Visit were handled.,Each instance of an observation present in the source data should be assigned this unique key. ,Yes,No,,,,,
OBSERVATION,person_id,Yes,integer,The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,,
OBSERVATION,observation_concept_id,Yes,integer,"The OBSERVATION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies.","The CONCEPT_ID that the OBSERVATION_SOURCE_CONCEPT_ID maps to. There is no specified domain that the Concepts in this table must adhere to. The only rule is that records with Concepts in the Condition, Procedure, Drug, Measurement, or Device domains MUST go to the corresponding table. ",No,Yes,CONCEPT,CONCEPT_ID,,,
OBSERVATION,observation_date,Yes,date,"The date of the Observation. Depending on what the Observation represents this could be the date of a lab test, the date of a survey, or the date a patient's family history was taken. ",For some observations the ETL may need to make a choice as to which date to choose.,No,No,,,,,
OBSERVATION,observation_datetime,No,datetime,,If no time is given set to midnight (00:00:00).,No,No,,,,,
OBSERVATION,observation_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Observation record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.","Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
OBSERVATION,observation_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Observation record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.","Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
OBSERVATION,value_as_number,No,float,"This is the numerical value of the Result of the Observation, if applicable and available. It is not expected that all Observations will have numeric results, rather, this field is here to house values should they exist. ",,No,No,,,,,
OBSERVATION,value_as_string,No,varchar(60),"This is the categorical value of the Result of the Observation, if applicable and available. ",,No,No,,,,,
OBSERVATION,value_as_concept_id,No,Integer,"It is possible that some records destined for the Observation table have two clinical ideas represented in one source code. This is common with ICD10 codes that describe a family history of some Condition, for example. In OMOP the Vocabulary breaks these two clinical ideas into two codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the VALUE_AS_CONCEPT_ID. It is important when using the Observation table to keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID field for relevant information. ","Note that the value of VALUE_AS_CONCEPT_ID may be provided through mapping from a source Concept which contains the content of the Observation. In those situations, the CONCEPT_RELATIONSHIP table in addition to the 'Maps to' record contains a second record with the relationship_id set to 'Maps to value'. For example, ICD10 [Z82.4](https://athena.ohdsi.org/search-terms/terms/45581076) 'Family history of ischaemic heart disease and other diseases of the circulatory system' has a 'Maps to' relationship to [4167217](https://athena.ohdsi.org/search-terms/terms/4167217) 'Family history of clinical finding' as well as a 'Maps to value' record to [134057](https://athena.ohdsi.org/search-terms/terms/134057) 'Disorder of cardiovascular system'.",No,Yes,CONCEPT,CONCEPT_ID,,,
@ -188,12 +188,12 @@ OBSERVATION,observation_source_concept_id,No,integer,"This is the concept repres
OBSERVATION,unit_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the unit of the Observation that occurred. ,This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,No,,,,,
OBSERVATION,qualifier_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the qualifier of the Observation that occurred. ,This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,No,,,,,
OBSERVATION,value_source_value,No,varchar(50),This field houses the verbatim result value of the Observation from the source data. Do not get confused with the Observation_source_value which captures source value of the observation mapped to observation_concept_id. This field is the observation result value from the source.," If the observation_source_value was a question, for example, or an observation that requires a result then this field is the answer/ result from the source data. Store the verbatim value that represents the result of the observation_source_value. ",No,No,,,,,
OBSERVATION,observation_event_id,No,bigint,"If the Observation record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here. See the [ETL Conventions for the OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm60.html#observation) table for more details.",No,No,,,,,
OBSERVATION,observation_event_id,No,integer,"If the Observation record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here. See the [ETL Conventions for the OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm60.html#observation) table for more details.",No,No,,,,,
OBSERVATION,obs_event_field_concept_id,No,integer,"If the Observation 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. ",Put the CONCEPT_ID that identifies which table and field the OBSERVATION_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,,,
DEATH,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
DEATH,death_date,Yes,date,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day.",No,No,,,,,
DEATH,death_datetime,No,datetime,,If not available set time to midnight (00:00:00),No,No,,,,,
DEATH,death_type_concept_id,No,integer,"This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.",Use the type concept that be reflects the source of the death record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
DEATH,death_type_concept_id,No,integer,"This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.",Use the type concept that be reflects the source of the death record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
DEATH,cause_concept_id,No,integer,"This is the Standard Concept representing the Person's cause of death, if available.","There is no specified domain for this concept, just choose the Standard Concept Id that best represents the person's cause of death.",No,Yes,CONCEPT,CONCEPT_ID,,,
DEATH,cause_source_value,No,varchar(50),,"If available, put the source code representing the cause of death here. ",No,No,,,,,
DEATH,cause_source_concept_id,No,integer,,If the cause of death was coded using a Vocabulary present in the OMOP Vocabularies put the CONCEPT_ID representing the cause of death here.,No,Yes,CONCEPT,CONCEPT_ID,,,
@ -201,7 +201,7 @@ NOTE,note_id,Yes,integer,A unique identifier for each note.,,Yes,No,,,,,
NOTE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
NOTE,note_date,Yes,date,The date the note was recorded.,,No,No,,,,,
NOTE,note_datetime,No,datetime,,If time is not given set the time to midnight.,No,No,,,,,
NOTE,note_type_concept_id,Yes,integer,The provenance of the note. Most likely this will be EHR. ,"Put the source system of the note, as in EHR record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
NOTE,note_type_concept_id,Yes,integer,The provenance of the note. Most likely this will be EHR. ,"Put the source system of the note, as in EHR record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
NOTE,note_class_concept_id,Yes,integer,"A Standard Concept Id representing the HL7 LOINC
Document Type Vocabulary classification of the note.",Map the note classification to a Standard Concept. For more information see the ETL Conventions in the description of the NOTE table. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&conceptClass=Doc+Kind&conceptClass=Doc+Role&conceptClass=Doc+Setting&conceptClass=Doc+Subject+Matter&conceptClass=Doc+Type+of+Service&domain=Meas+Value&page=1&pageSize=15&query=). This Concept can alternatively be represented by concepts with the relationship 'Kind of (LOINC)' to [706391](https://athena.ohdsi.org/search-terms/terms/706391) (Note).,No,Yes,CONCEPT,CONCEPT_ID,,,
NOTE,note_title,No,varchar(250),The title of the note.,,No,No,,,,,
@ -212,7 +212,7 @@ NOTE,provider_id,No,integer,The Provider who wrote the note.,The ETL may need to
NOTE,visit_occurrence_id,No,integer,The Visit during which the note was written. ,,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,
NOTE,visit_detail_id,No,integer,The Visit Detail during which the note was written.,,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,,
NOTE,note_source_value,No,varchar(50),,The source value mapped to the NOTE_CLASS_CONCEPT_ID.,No,No,,,,,
NOTE,note_event_id,No,bigint,"If the Note record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here.",No,No,,,,,
NOTE,note_event_id,No,integer,"If the Note record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here.",No,No,,,,,
NOTE,note_event_field_concept_id,No,integer,"If the Note 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. ",Put the CONCEPT_ID that identifies which table and field the NOTE_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,,,
NOTE_NLP,note_nlp_id,Yes,integer,A unique identifier for the NLP record.,,Yes,No,,,,,
NOTE_NLP,note_id,Yes,integer,This is the NOTE_ID for the NOTE record the NLP record is associated to.,,No,No,,,,,
@ -245,7 +245,7 @@ NOTE_NLP,term_modifiers,No,varchar(2000),,"For the modifiers that are there, the
SPECIMEN,specimen_id,Yes,integer,Unique identifier for each specimen.,,Yes,No,,,,,
SPECIMEN,person_id,Yes,integer,The person from whom the specimen is collected.,,No,Yes,PERSON,PERSON_ID,,,
SPECIMEN,specimen_concept_id,Yes,integer,,The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the specimen domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Specimen&standardConcept=Standard&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,,,
SPECIMEN,specimen_type_concept_id,Yes,integer,,"Put the source of the specimen record, as in an EHR system. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
SPECIMEN,specimen_type_concept_id,Yes,integer,,"Put the source of the specimen record, as in an EHR system. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
SPECIMEN,specimen_date,Yes,date,The date the specimen was collected.,,No,No,,,,,
SPECIMEN,specimen_datetime,No,datetime,,,No,No,,,,,
SPECIMEN,quantity,No,float,The amount of specimen collected from the person.,,No,No,,,,,
@ -274,7 +274,7 @@ LOCATION,country_concept_id,No,integer,The Concept Id representing the country.
LOCATION,country_source_value,No,varchar(80),The name of the country.,,No,No,,,,,
LOCATION,latitude,No,float,,Must be between -90 and 90.,No,No,,,,,
LOCATION,longitude,No,float,,Must be between -180 and 180.,No,No,,,,,
CARE_SITE,care_site_id,Yes,integer,,Assign an id to each unique combination of location_id and place_of_service_source_value,Yes,No,,,,,
CARE_SITE,care_site_id,Yes,integer,,"Assign an ID to each combination of a location and nature of the site - the latter could be the Place of Service, name or another characteristic in your source data.",Yes,No,,,,,
CARE_SITE,care_site_name,No,varchar(255),The name of the care_site as it appears in the source data,,No,No,,,,,
CARE_SITE,place_of_service_concept_id,No,integer,"This is a high-level way of characterizing a Care Site. Typically, however, Care Sites can provide care in multiple settings (inpatient, outpatient, etc.) and this granularity should be reflected in the visit.","Choose the concept in the visit domain that best represents the setting in which healthcare is provided in the Care Site. If most visits in a Care Site are Inpatient, then the place_of_service_concept_id should represent Inpatient. If information is present about a unique Care Site (e.g. Pharmacy) then a Care Site record should be created. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=2&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,,
CARE_SITE,location_id,No,integer,The location_id from the LOCATION table representing the physical location of the care_site.,,No,Yes,LOCATION,LOCATION_ID,,,
@ -367,21 +367,21 @@ Condition.",,No,No,,,,,
CONDITION_ERA,condition_occurrence_count,No,integer,"The number of individual Condition
Occurrences used to construct the
condition era.",,No,No,,,,,
EPISODE,episode_id,Yes,bigint,A unique identifier for each Episode.,,Yes,No,,,,,
EPISODE,person_id,Yes,bigint,The PERSON_ID of the PERSON for whom the episode is recorded.,,No,Yes,PERSON,PERSON_ID,,,
EPISODE,episode_id,Yes,integer,A unique identifier for each Episode.,,Yes,No,,,,,
EPISODE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the episode is recorded.,,No,Yes,PERSON,PERSON_ID,,,
EPISODE,episode_concept_id,Yes,integer,"The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.","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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Episode&page=1&pageSize=15&query=)",No,Yes,CONCEPT,CONCEPT_ID,Episode,,
EPISODE,episode_start_date,Yes,date,The date when the Episode beings. ,Please see [article] for how to define an Episode start date.,No,No,,,,,
EPISODE,episode_start_datetime,No,datetime,The date and time when the Episode begins.,,No,No,,,,,
EPISODE,episode_end_date,No,date,The date when the instance of the Episode is considered to have ended.,Please see [article] for how to define an Episode end date.,No,No,,,,,
EPISODE,episode_end_datetime,No,datetime,The date when the instance of the Episode is considered to have ended.,,No,No,,,,,
EPISODE,episode_parent_id,No,bigint,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.,"If there are multiple nested levels to how Episodes are represented, the EPISODE_PARENT_ID can be used to record this relationship. ",No,No,,,,,
EPISODE,episode_parent_id,No,integer,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.,"If there are multiple nested levels to how Episodes are represented, the EPISODE_PARENT_ID can be used to record this relationship. ",No,No,,,,,
EPISODE,episode_number,No,integer,"For sequences of episodes, this is used to indicate the order the episodes occurred. For example, lines of treatment could be indicated here. ",Please see [article] for the details of how to count episodes.,No,No,,,,,
EPISODE,episode_object_concept_id,Yes,integer,"A Standard Concept representing the disease phase, outcome, or other abstraction of which the episode consists. For example, if the EPISODE_CONCEPT_ID is [treatment regimen](https://athena.ohdsi.org/search-terms/terms/32531) then the EPISODE_OBJECT_CONCEPT_ID should contain the chemotherapy regimen concept, like [Afatinib monotherapy](https://athena.ohdsi.org/search-terms/terms/35804392). ",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.,No,Yes,CONCEPT,CONCEPT_ID,"Procedure, Regimen",,
EPISODE,episode_type_concept_id,Yes,integer,"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.",Choose the EPISODE_TYPE_CONCEPT_ID that best represents the provenance of the record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
EPISODE,episode_type_concept_id,Yes,integer,"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.",Choose the EPISODE_TYPE_CONCEPT_ID that best represents the provenance of the record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
EPISODE,episode_source_value,No,varchar(50),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.,,No,No,,,,,
EPISODE,episode_source_concept_id,No,integer,A foreign key to a Episode Concept that refers to the code used in the source.,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. ,No,Yes,CONCEPT,CONCEPT_ID,,,
EPISODE_EVENT,episode_id,Yes,bigint,Use this field to link the EPISODE_EVENT record to its EPISODE.,Put the EPISODE_ID that subsumes the EPISODE_EVENT record here.,No,Yes,EPISODE,EPISODE_ID,,,
EPISODE_EVENT,event_id,Yes,bigint,"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. ",Put the primary key of the linked record here. ,No,No,,,,,
EPISODE_EVENT,episode_id,Yes,integer,Use this field to link the EPISODE_EVENT record to its EPISODE.,Put the EPISODE_ID that subsumes the EPISODE_EVENT record here.,No,Yes,EPISODE,EPISODE_ID,,,
EPISODE_EVENT,event_id,Yes,integer,"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. ",Put the primary key of the linked record here. ,No,No,,,,,
EPISODE_EVENT,episode_event_field_concept_id,Yes,integer,This field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. ,Put the CONCEPT_ID that identifies which table and field the EVENT_ID came from. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?vocabulary=CDM&conceptClass=Field&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,Metadata,,
METADATA,metadata_id,Yes,integer,The unique key given to a Metadata record.,Attribute value is auto-generated,Yes,No,,,,,
METADATA,metadata_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
@ -401,8 +401,8 @@ CDM_SOURCE,cdm_etl_reference,No,varchar(255),,Put the link to the CDM version us
CDM_SOURCE,source_release_date,Yes,date,The release date of the source data.,,No,No,,,,,
CDM_SOURCE,cdm_release_date,Yes,date,The release data of the CDM instance.,,No,No,,,,,
CDM_SOURCE,cdm_version,No,varchar(10),,,No,No,,,,,
CDM_SOURCE,cdm_version_concept_id,Yes,integer,The Concept Id representing the version of the CDM.,,No,Yes,CONCEPT,CONCEPT_ID,,,
CDM_SOURCE,vocabulary_version,Yes,varchar(20),,,No,No,,,,,
CDM_SOURCE,cdm_version_concept_id,Yes,integer,The Concept Id representing the version of the CDM.,You can find all concepts that represent the CDM versions using the query: SELECT * FROM CONCEPT WHERE VOCABULARY_ID = 'CDM' AND CONCEPT_CLASS = 'CDM',No,Yes,CONCEPT,CONCEPT_ID,,,
CDM_SOURCE,vocabulary_version,Yes,varchar(20),,You can find the version of your Vocabulary using the query: SELECT vocabulary_version from vocabulary where vocabulary_id = 'None',No,No,,,,,
CONCEPT,concept_id,Yes,integer,A unique identifier for each Concept across all domains.,,Yes,No,,,,,
CONCEPT,concept_name,Yes,varchar(255),"An unambiguous, meaningful and descriptive name for the Concept.",,No,No,,,,,
CONCEPT,domain_id,Yes,varchar(20),A foreign key to the [DOMAIN](https://ohdsi.github.io/CommonDataModel/cdm531.html#domain) table the Concept belongs to.,,No,Yes,DOMAIN,DOMAIN_ID,,,

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
21 OBSERVATION_PERIOD person_id Yes integer The Person ID of the PERSON record for which the Observation Period is recorded. No Yes PERSON PERSON_ID
22 OBSERVATION_PERIOD observation_period_start_date Yes date Use this date to determine the start date of the Observation Period. It is often the case that the idea of Observation Periods does not exist in source data. In those cases, the observation_period_start_date can be inferred as the earliest Event date available for the Person. In insurance claim data, the Observation Period can be considered as the time period the Person is enrolled with a payer. If a Person switches plans but stays with the same payer, and therefore capturing of data continues, that change would be captured in [PAYER_PLAN_PERIOD](https://ohdsi.github.io/CommonDataModel/cdm531.html#payer_plan_period). No No
23 OBSERVATION_PERIOD observation_period_end_date Yes date Use this date to determine the end date of the period for which we can assume that all events for a Person are recorded. It is often the case that the idea of Observation Periods does not exist in source data. In those cases, the observation_period_end_date can be inferred as the last Event date available for the Person. In insurance claim data, the Observation Period can be considered as the time period the Person is enrolled with a payer. No No
24 OBSERVATION_PERIOD period_type_concept_id Yes integer This field can be used to determine the provenance of the Observation Period as in whether the period was determined from an insurance enrollment file, EHR healthcare encounters, or other sources. Choose the observation_period_type_concept_id that best represents how the period was determined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). Choose the observation_period_type_concept_id that best represents how the period was determined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). No Yes CONCEPT CONCEPT_ID Type Concept
25 VISIT_OCCURRENCE visit_occurrence_id Yes integer Use this to identify unique interactions between a person and the health care system. This identifier links across the other CDM event tables to associate events with a visit. This should be populated by creating a unique identifier for each unique interaction between a person and the healthcare system where the person receives a medical good or service over a span of time. Yes No
26 VISIT_OCCURRENCE person_id Yes integer No Yes PERSON PERSON_ID
27 VISIT_OCCURRENCE visit_concept_id Yes integer This field contains a concept id representing the kind of visit, like inpatient or outpatient. All concepts in this field should be standard and belong to the Visit domain. Populate this field based on the kind of visit that took place for the person. For example this could be "Inpatient Visit", "Outpatient Visit", "Ambulatory Visit", etc. This table will contain standard concepts in the Visit domain. These concepts are arranged in a hierarchical structure to facilitate cohort definitions by rolling up to generally familiar Visits adopted in most healthcare systems worldwide. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID Visit
35 VISIT_OCCURRENCE visit_source_value No varchar(50) This field houses the verbatim value from the source data representing the kind of visit that took place (inpatient, outpatient, emergency, etc.) If there is information about the kind of visit in the source data that value should be stored here. If a visit is an amalgamation of visits from the source then use a hierarchy to choose the visit source value, such as IP -> ER-> OP. This should line up with the logic chosen to determine how visits are created. No No
36 VISIT_OCCURRENCE visit_source_concept_id No integer If the visit source value is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. No Yes CONCEPT CONCEPT_ID
37 VISIT_OCCURRENCE admitted_from_concept_id No integer Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example. If available, map the admitted_from_source_value to a standard concept in the visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=). If a person was admitted from home, set this to 0. No Yes CONCEPT CONCEPT_ID Visit
38 VISIT_OCCURRENCE admitted_from_source_value No varchar(50) This information may be called something different in the source data but the field is meant to contain a value indicating where a person was admitted from. Typically this applies only to visits that have a length of stay, like inpatient visits or long-term care visits. No No
39 VISIT_OCCURRENCE discharged_to_concept_id No integer Use this field to determine where the patient was discharged to after a visit. This concept is part of the visit domain and can indicate if a patient was transferred to another hospital or sent to a long-term care facility, for example. It is assumed that a person is discharged to home therefore there is not a standard concept id for "home". Use concept id = 0 when a person is discharged to home. If available, map the discharged_to_source_value to a standard concept in the visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID Visit
40 VISIT_OCCURRENCE discharged_to_source_value No varchar(50) This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more. No No
41 VISIT_OCCURRENCE preceding_visit_occurrence_id No integer Use this field to find the visit that occurred for the person prior to the given visit. There could be a few days or a few years in between. This field can be used to link a visit immediately preceding the current visit. Note this is not symmetrical, and there is no such thing as a "following_visit_id". No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID
58 VISIT_DETAIL preceding_visit_detail_id No integer Use this field to find the visit detail that occurred for the person prior to the given visit detail record. There could be a few days or a few years in between. The PRECEDING_VISIT_DETAIL_ID can be used to link a visit immediately preceding the current Visit Detail. Note this is not symmetrical, and there is no such thing as a "following_visit_id". No Yes VISIT_DETAIL VISIT_DETAIL_ID
59 VISIT_DETAIL parent_visit_detail_id No integer Use this field to find the visit detail that subsumes the given visit detail record. This is used in the case that a visit detail record needs to be nested beyond the VISIT_OCCURRENCE/VISIT_DETAIL relationship. If there are multiple nested levels to how Visits are represented in the source, the VISIT_DETAIL_PARENT_ID can be used to record this relationship. No Yes VISIT_DETAIL VISIT_DETAIL_ID
60 VISIT_DETAIL visit_occurrence_id Yes integer Use this field to link the VISIT_DETAIL record to its VISIT_OCCURRENCE. Put the VISIT_OCCURRENCE_ID that subsumes the VISIT_DETAIL record here. No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID
61 CONDITION_OCCURRENCE condition_occurrence_id Yes integer The unique key given to a condition record for a person. Refer to the ETL for how duplicate conditions during the same visit were handled. Each instance of a condition present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same condition within the same visit. It is valid to keep these duplicates and assign them individual, unique, CONDITION_OCCURRENCE_IDs, though it is up to the ETL how they should be handled. Yes No
62 CONDITION_OCCURRENCE person_id Yes integer The PERSON_ID of the PERSON for whom the condition is recorded. No Yes PERSON PERSON_ID
63 CONDITION_OCCURRENCE condition_concept_id Yes integer The CONDITION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a condition The CONCEPT_ID that the CONDITION_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of "Condition" should go in this table. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Condition&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID Condition
64 CONDITION_OCCURRENCE condition_start_date Yes date Use this date to determine the start date of the condition Most often data sources do not have the idea of a start date for a condition. Rather, if a source only has one date associated with a condition record it is acceptable to use that date for both the CONDITION_START_DATE and the CONDITION_END_DATE. No No
77 DRUG_EXPOSURE drug_exposure_id Yes integer The unique key given to records of drug dispensings or administrations for a person. Refer to the ETL for how duplicate drugs during the same visit were handled. Each instance of a drug dispensing or administration present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same drug within the same visit. It is valid to keep these duplicates and assign them individual, unique, DRUG_EXPOSURE_IDs, though it is up to the ETL how they should be handled. Yes No
78 DRUG_EXPOSURE person_id Yes integer The PERSON_ID of the PERSON for whom the drug dispensing or administration is recorded. This may be a system generated code. No Yes PERSON PERSON_ID
79 DRUG_EXPOSURE drug_concept_id Yes integer The DRUG_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a drug product or molecule otherwise introduced to the body. The drug concepts can have a varying degree of information about drug strength and dose. This information is relevant in the context of quantity and administration information in the subsequent fields plus strength information from the DRUG_STRENGTH table, provided as part of the standard vocabulary download. The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should be derived either from mapping from the source concept id or by picking the drug concept representing the most amount of detail you have. Records whose source values map to standard concepts with a domain of Drug should go in this table. When the Drug Source Value of the code cannot be translated into Standard Drug Concept IDs, a Drug exposure entry is stored with only the corresponding SOURCE_CONCEPT_ID and DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the most detailed content of information is preferred during the mapping process. These are indicated in the CONCEPT_CLASS_ID field of the Concept and are recorded in the following order of precedence: 'Branded Pack', 'Clinical Pack', 'Branded Drug', 'Clinical Drug', 'Branded Drug Component', 'Clinical Drug Component', 'Branded Drug Form', 'Clinical Drug Form', and only if no other information is available 'Ingredient'. Note: If only the drug class is known, the DRUG_CONCEPT_ID field should contain 0. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID Drug
80 DRUG_EXPOSURE drug_exposure_start_date Yes date Use this date to determine the start date of the drug record. Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration was recorded. It is a valid ETL choice to use the date the drug was ordered as the DRUG_EXPOSURE_START_DATE. No No
81 DRUG_EXPOSURE drug_exposure_start_datetime No datetime This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) No No
82 DRUG_EXPOSURE drug_exposure_end_date Yes date The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient. If this information is not explicitly available in the data, infer the end date using the following methods:<br><br> 1. Start first with duration or days supply using the calculation drug start date + days supply -1 day. 2. Use quantity divided by daily dose that you may obtain from the sig or a source field (or assumed daily dose of 1) for solid, indivisibile, drug products. If quantity represents ingredient amount, quantity divided by daily dose * concentration (from drug_strength) drug concept id tells you the dose form. 3. If it is an administration record, set drug end date equal to drug start date. If the record is a written prescription then set end date to start date + 29. If the record is a mail-order prescription set end date to start date + 89. The end date must be equal to or greater than the start date. Ibuprofen 20mg/mL oral solution concept tells us this is oral solution. Calculate duration as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL) 200*5/20 = 50 days. [Examples by dose form](https://ohdsi.github.io/CommonDataModel/drug_dose.html) No No
83 DRUG_EXPOSURE drug_exposure_end_datetime No datetime This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) No No
94 DRUG_EXPOSURE visit_occurrence_id No integer The Visit during which the drug was prescribed, administered or dispensed. To populate this field drug exposures must be explicitly initiated in the visit. No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID
95 DRUG_EXPOSURE visit_detail_id No integer The VISIT_DETAIL record during which the drug exposure occurred. For example, if the person was in the ICU at the time of the drug administration the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit. Same rules apply as for the VISIT_OCCURRENCE_ID. No Yes VISIT_DETAIL VISIT_DETAIL_ID
96 DRUG_EXPOSURE drug_source_value No varchar(50) This field houses the verbatim value from the source data representing the drug exposure that occurred. For example, this could be an NDC or Gemscript code. This code is mapped to a Standard Drug Concept in the Standardized Vocabularies and the original code is stored here for reference. No No
97 DRUG_EXPOSURE drug_source_concept_id No integer This is the concept representing the drug source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Drug necessary for a given analytic use case. Consider using DRUG_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. If the DRUG_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. No Yes CONCEPT CONCEPT_ID
98 DRUG_EXPOSURE route_source_value No varchar(50) This field houses the verbatim value from the source data representing the drug route. This information may be called something different in the source data but the field is meant to contain a value indicating when and how a drug was given to a patient. This source value is mapped to a standard concept which is stored in the ROUTE_CONCEPT_ID field. No No
99 DRUG_EXPOSURE dose_unit_source_value No varchar(50) This field houses the verbatim value from the source data representing the dose unit of the drug given. This information may be called something different in the source data but the field is meant to contain a value indicating the unit of dosage of drug given to the patient. **This is an older column and will be deprecated in an upcoming version.** No No
100 PROCEDURE_OCCURRENCE procedure_occurrence_id Yes integer The unique key given to a procedure record for a person. Refer to the ETL for how duplicate procedures during the same visit were handled. Each instance of a procedure occurrence in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same procedure within the same visit. It is valid to keep these duplicates and assign them individual, unique, PROCEDURE_OCCURRENCE_IDs, though it is up to the ETL how they should be handled. Yes No
118 DEVICE_EXPOSURE device_concept_id Yes integer The DEVICE_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a foreign object or instrument the person was exposed to. The CONCEPT_ID that the DEVICE_SOURCE_VALUE maps to. No Yes CONCEPT CONCEPT_ID Device
119 DEVICE_EXPOSURE device_exposure_start_date Yes date Use this date to determine the start date of the device record. Valid entries include a start date of a procedure to implant a device, the date of a prescription for a device, or the date of device administration. No No
120 DEVICE_EXPOSURE device_exposure_start_datetime No datetime This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) No No
121 DEVICE_EXPOSURE device_exposure_end_date No date The DEVICE_EXPOSURE_END_DATE denotes the day the device exposure ended for the patient, if given. Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable. No No
122 DEVICE_EXPOSURE device_exposure_end_datetime No datetime If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) No No
123 DEVICE_EXPOSURE device_type_concept_id Yes integer You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR. Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). No Yes CONCEPT CONCEPT_ID Type Concept
124 DEVICE_EXPOSURE unique_device_id No varchar(255) This is the Unique Device Identification (UDI-DI) number for devices regulated by the FDA, if given. For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field. No No
134 DEVICE_EXPOSURE unit_source_concept_id No integer This is the concept representing the UNIT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Unit necessary for a given analytic use case. Consider using UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. No Yes CONCEPT CONCEPT_ID
135 MEASUREMENT measurement_id Yes integer The unique key given to a Measurement record for a Person. Refer to the ETL for how duplicate Measurements during the same Visit were handled. Each instance of a measurement present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same measurement within the same visit. It is valid to keep these duplicates and assign them individual, unique, MEASUREMENT_IDs, though it is up to the ETL how they should be handled. Yes No
136 MEASUREMENT person_id Yes integer The PERSON_ID of the Person for whom the Measurement is recorded. This may be a system generated code. No Yes PERSON PERSON_ID
137 MEASUREMENT measurement_concept_id Yes integer The MEASUREMENT_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. The CONCEPT_ID that the MEASUREMENT_SOURCE_CONCEPT_ID maps to. Only records whose SOURCE_CONCEPT_IDs map to Standard Concepts with a domain of "Measurement" should go in this table. No Yes CONCEPT CONCEPT_ID Measurement
138 MEASUREMENT measurement_date Yes date Use this date to determine the date of the measurement. If there are multiple dates in the source data associated with a record such as order_date, draw_date, and result_date, choose the one that is closest to the date the sample was drawn from the patient. No No
139 MEASUREMENT measurement_datetime No datetime This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000) No No
140 MEASUREMENT measurement_time No varchar(10) This is present for backwards compatibility and will be deprecated in an upcoming version. No No
152 MEASUREMENT measurement_source_concept_id No integer This is the concept representing the MEASUREMENT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Measurement necessary for a given analytic use case. Consider using MEASUREMENT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. If the MEASUREMENT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. No Yes CONCEPT CONCEPT_ID
153 MEASUREMENT unit_source_value No varchar(50) This field houses the verbatim value from the source data representing the unit of the Measurement that occurred. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. No No
154 MEASUREMENT unit_source_concept_id No integer "This is the concept representing the UNIT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Measurement necessary for a given analytic use case. Consider using UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network." If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. No Yes CONCEPT CONCEPT_ID
155 MEASUREMENT value_source_value No varchar(50) This field houses the verbatim result value of the Measurement from the source data . If both a continuous and categorical result are given in the source data such that both VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are both included, store the verbatim value that was mapped to VALUE_AS_CONCEPT_ID here. No No
156 MEASUREMENT measurement_event_id No bigint integer If the Measurement record is related to another record in the database, this field is the primary key of the linked record. Put the primary key of the linked record, if applicable, here. No No
157 MEASUREMENT meas_event_field_concept_id No integer 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. Put the CONCEPT_ID that identifies which table and field the MEASUREMENT_EVENT_ID came from. No Yes CONCEPT CONCEPT_ID
158 OBSERVATION observation_id Yes integer The unique key given to an Observation record for a Person. Refer to the ETL for how duplicate Observations during the same Visit were handled. Each instance of an observation present in the source data should be assigned this unique key. Yes No
167 OBSERVATION qualifier_concept_id No integer This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc. Use your best judgement as to what Concepts to use here and if they are necessary to accurately represent the clinical record. There is no restriction on the domain of these Concepts, they just need to be Standard. No Yes CONCEPT CONCEPT_ID
168 OBSERVATION unit_concept_id No integer 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. 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. No Yes CONCEPT CONCEPT_ID Unit
169 OBSERVATION provider_id No integer The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result. The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record. For example the admitting vs attending physician on an EHR record. No Yes PROVIDER PROVIDER_ID
170 OBSERVATION visit_occurrence_id No integer The visit during which the Observation occurred. Depending on the structure of the source data, this may have to be determined based on dates. If an OBSERVATION_DATE occurs within the start and end date of a Visit it is a valid ETL choice to choose the VISIT_OCCURRENCE_ID from the visit that subsumes it, even if not explicitly stated in the data. While not required, an attempt should be made to locate the VISIT_OCCURRENCE_ID of the observation record. If an observation is related to a visit explicitly in the source data, it is possible that the result date of the Observation falls outside of the bounds of the Visit dates. No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID
171 OBSERVATION visit_detail_id No integer The VISIT_DETAIL record during which the Observation occurred. For example, if the Person was in the ICU at the time the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit. Same rules apply as for the VISIT_OCCURRENCE_ID. No Yes VISIT_DETAIL VISIT_DETAIL_ID
172 OBSERVATION observation_source_value No varchar(50) This field houses the verbatim value from the source data representing the Observation that occurred. For example, this could be an ICD10 or Read code. This code is mapped to a Standard Concept in the Standardized Vocabularies and the original code is stored here for reference. No No
173 OBSERVATION observation_source_concept_id No integer This is the concept representing the OBSERVATION_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Observation necessary for a given analytic use case. Consider using OBSERVATION_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. If the OBSERVATION_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. No Yes CONCEPT CONCEPT_ID
174 OBSERVATION unit_source_value No varchar(50) This field houses the verbatim value from the source data representing the unit of the Observation that occurred. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. No No
175 OBSERVATION qualifier_source_value No varchar(50) This field houses the verbatim value from the source data representing the qualifier of the Observation that occurred. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. No No
176 OBSERVATION value_source_value No varchar(50) This field houses the verbatim result value of the Observation from the source data. Do not get confused with the Observation_source_value which captures source value of the observation mapped to observation_concept_id. This field is the observation result value from the source. If the observation_source_value was a question, for example, or an observation that requires a result then this field is the answer/ result from the source data. Store the verbatim value that represents the result of the observation_source_value. No No
177 OBSERVATION observation_event_id No bigint integer If the Observation record is related to another record in the database, this field is the primary key of the linked record. Put the primary key of the linked record, if applicable, here. See the [ETL Conventions for the OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm60.html#observation) table for more details. No No
178 OBSERVATION obs_event_field_concept_id No integer If the Observation 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. Put the CONCEPT_ID that identifies which table and field the OBSERVATION_EVENT_ID came from. No Yes CONCEPT CONCEPT_ID
179 DEATH person_id Yes integer No Yes PERSON PERSON_ID
180 DEATH death_date Yes date The date the person was deceased. If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day. No No
188 NOTE note_date Yes date The date the note was recorded. No No
189 NOTE note_datetime No datetime If time is not given set the time to midnight. No No
190 NOTE note_type_concept_id Yes integer The provenance of the note. Most likely this will be EHR. Put the source system of the note, as in EHR record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=). Put the source system of the note, as in EHR record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). No Yes CONCEPT CONCEPT_ID Type Concept
191 NOTE note_class_concept_id Yes integer A Standard Concept Id representing the HL7 LOINC Document Type Vocabulary classification of the note. Map the note classification to a Standard Concept. For more information see the ETL Conventions in the description of the NOTE table. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&conceptClass=Doc+Kind&conceptClass=Doc+Role&conceptClass=Doc+Setting&conceptClass=Doc+Subject+Matter&conceptClass=Doc+Type+of+Service&domain=Meas+Value&page=1&pageSize=15&query=). This Concept can alternatively be represented by concepts with the relationship 'Kind of (LOINC)' to [706391](https://athena.ohdsi.org/search-terms/terms/706391) (Note). No Yes CONCEPT CONCEPT_ID
192 NOTE note_title No varchar(250) The title of the note. No No
193 NOTE note_text Yes varchar(MAX) The content of the note. No No
194 NOTE encoding_concept_id Yes integer This is the Concept representing the character encoding type. Put the Concept Id that represents the encoding character type here. Currently the only option is UTF-8 ([32678](https://athena.ohdsi.org/search-terms/terms/32678)). It the note is encoded in any other type, like ASCII then put 0. No Yes CONCEPT CONCEPT_ID
195 NOTE language_concept_id Yes integer The language of the note. Use Concepts that are descendants of the concept [4182347](https://athena.ohdsi.org/search-terms/terms/4182347) (World Languages). No Yes CONCEPT CONCEPT_ID
196 NOTE provider_id No integer The Provider who wrote the note. The ETL may need to make a determination on which provider to put here. No Yes PROVIDER PROVIDER_ID
197 NOTE visit_occurrence_id No integer The Visit during which the note was written. No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID
198 NOTE visit_detail_id No integer The Visit Detail during which the note was written. No Yes VISIT_DETAIL VISIT_DETAIL_ID
199 NOTE note_source_value No varchar(50) The source value mapped to the NOTE_CLASS_CONCEPT_ID. No No
201 NOTE note_event_field_concept_id No integer If the Note 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. Put the CONCEPT_ID that identifies which table and field the NOTE_EVENT_ID came from. No Yes CONCEPT CONCEPT_ID
202 NOTE_NLP note_nlp_id Yes integer A unique identifier for the NLP record. Yes No
203 NOTE_NLP note_id Yes integer This is the NOTE_ID for the NOTE record the NLP record is associated to. No No
204 NOTE_NLP section_concept_id No integer The SECTION_CONCEPT_ID should be used to represent the note section contained in the NOTE_NLP record. These concepts can be found as parts of document panels and are based on the type of note written, i.e. a discharge summary. These panels can be found as concepts with the relationship 'Subsumes' to CONCEPT_ID [45875957](https://athena.ohdsi.org/search-terms/terms/45875957). No Yes CONCEPT CONCEPT_ID
205 NOTE_NLP snippet No varchar(250) A small window of text surrounding the term No No
206 NOTE_NLP "offset" No varchar(50) Character offset of the extracted term in the input note No No
207 NOTE_NLP lexical_variant Yes varchar(250) Raw text extracted from the NLP tool. No No
212 NOTE_NLP nlp_datetime No datetime The date and time of the note processing. No No
213 NOTE_NLP term_exists No varchar(1) Term_exists is defined as a flag that indicates if the patient actually has or had the condition. Any of the following modifiers would make Term_exists false: Negation = true Subject = [anything other than the patient] Conditional = true/li> Rule_out = true Uncertain = very low certainty or any lower certainties A complete lack of modifiers would make Term_exists true. No No
214 NOTE_NLP term_temporal No varchar(50) Term_temporal is to indicate if a condition is present or just in the past. The following would be past:<br><br> - History = true - Concept_date = anything before the time of the report No No
215 NOTE_NLP term_modifiers No varchar(2000) For the modifiers that are there, they would have to have these values:<br><br> - Negation = false - Subject = patient - Conditional = false - Rule_out = false - Uncertain = true or high or moderate or even low (could argue about low). Term_modifiers will concatenate all modifiers for different types of entities (conditions, drugs, labs etc) into one string. Lab values will be saved as one of the modifiers. No No
216 SPECIMEN specimen_id Yes integer Unique identifier for each specimen. Yes No
217 SPECIMEN person_id Yes integer The person from whom the specimen is collected. No Yes PERSON PERSON_ID
218 SPECIMEN specimen_concept_id Yes integer The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the specimen domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Specimen&standardConcept=Standard&page=1&pageSize=15&query=) No Yes CONCEPT CONCEPT_ID
245 LOCATION country_source_value No varchar(80) The name of the country. No No
246 LOCATION latitude No float Must be between -90 and 90. No No
247 LOCATION longitude No float Must be between -180 and 180. No No
248 CARE_SITE care_site_id Yes integer Assign an id to each unique combination of location_id and place_of_service_source_value Assign an ID to each combination of a location and nature of the site - the latter could be the Place of Service, name or another characteristic in your source data. Yes No
249 CARE_SITE care_site_name No varchar(255) The name of the care_site as it appears in the source data No No
250 CARE_SITE place_of_service_concept_id No integer This is a high-level way of characterizing a Care Site. Typically, however, Care Sites can provide care in multiple settings (inpatient, outpatient, etc.) and this granularity should be reflected in the visit. Choose the concept in the visit domain that best represents the setting in which healthcare is provided in the Care Site. If most visits in a Care Site are Inpatient, then the place_of_service_concept_id should represent Inpatient. If information is present about a unique Care Site (e.g. Pharmacy) then a Care Site record should be created. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=2&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID
251 CARE_SITE location_id No integer The location_id from the LOCATION table representing the physical location of the care_site. No Yes LOCATION LOCATION_ID
274 PAYER_PLAN_PERIOD plan_concept_id No integer This field represents the specific health benefit Plan the Person is enrolled in. Map the Plan directly to a standard CONCEPT_ID. If one does not exists please contact the vocabulary team. There is no global controlled vocabulary available for this information. The point is to stratify on this information and identify if Persons have the same health benefit Plan though the name of the Plan is not necessary. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Plan&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID
275 PAYER_PLAN_PERIOD plan_source_value No varchar(50) This is the health benefit Plan of the Person as it appears in the source data. No No
276 PAYER_PLAN_PERIOD plan_source_concept_id No integer If the source data codes the Plan in an OMOP supported vocabulary store the concept_id here. No Yes CONCEPT CONCEPT_ID
277 PAYER_PLAN_PERIOD sponsor_concept_id No integer This field represents the sponsor of the Plan who finances the Plan. This includes self-insured, small group health plan and large group health plan. Map the sponsor directly to a standard CONCEPT_ID. If one does not exists please contact the vocabulary team. There is no global controlled vocabulary available for this information. The point is to stratify on this information and identify if Persons have the same sponsor though the name of the sponsor is not necessary. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Sponsor&standardConcept=Standard&page=1&pageSize=15&query=). No Yes CONCEPT CONCEPT_ID
278 PAYER_PLAN_PERIOD sponsor_source_value No varchar(50) The Plan sponsor as it appears in the source data. No No
279 PAYER_PLAN_PERIOD sponsor_source_concept_id No integer If the source data codes the sponsor in an OMOP supported vocabulary store the concept_id here. No Yes CONCEPT CONCEPT_ID
280 PAYER_PLAN_PERIOD family_source_value No varchar(50) The common identifier for all people (often a family) that covered by the same policy. Often these are the common digits of the enrollment id of the policy members. No No
367 CONCEPT standard_concept No varchar(1) This flag determines where a Concept is a Standard Concept, i.e. is used in the data, a Classification Concept, or a non-standard Source Concept. The allowable values are 'S' (Standard Concept) and 'C' (Classification Concept), otherwise the content is NULL. No No
368 CONCEPT concept_code Yes varchar(50) The concept code represents the identifier of the Concept in the source vocabulary, such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note that concept codes are not unique across vocabularies. No No
369 CONCEPT valid_start_date Yes date The date when the Concept was first recorded. The default value is 1-Jan-1970, meaning, the Concept has no (known) date of inception. No No
370 CONCEPT valid_end_date Yes date The date when the Concept became invalid because it was deleted or superseded (updated) by a new concept. The default value is 31-Dec-2099, meaning, the Concept is valid until it becomes deprecated. No No
371 CONCEPT invalid_reason No varchar(1) Reason the Concept was invalidated. Possible values are D (deleted), U (replaced with an update) or NULL when valid_end_date has the default value. No No
372 VOCABULARY vocabulary_id Yes varchar(20) A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. Yes No
373 VOCABULARY vocabulary_name Yes varchar(255) The name describing the vocabulary, for example, International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) etc. No No
374 VOCABULARY vocabulary_reference No varchar(255) External reference to documentation or available download of the about the vocabulary. No No
375 VOCABULARY vocabulary_version No varchar(255) Version of the Vocabulary as indicated in the source. No No
376 VOCABULARY vocabulary_concept_id Yes integer A Concept that represents the Vocabulary the VOCABULARY record belongs to. No Yes CONCEPT CONCEPT_ID
377 DOMAIN domain_id Yes varchar(20) A unique key for each domain. Yes No
378 DOMAIN domain_name Yes varchar(255) The name describing the Domain, e.g. Condition, Procedure, Measurement etc. No No
379 DOMAIN domain_concept_id Yes integer A Concept representing the Domain Concept the DOMAIN record belongs to. No Yes CONCEPT CONCEPT_ID
380 CONCEPT_CLASS concept_class_id Yes varchar(20) A unique key for each class. Yes No
381 CONCEPT_CLASS concept_class_name Yes varchar(255) The name describing the Concept Class, e.g. Clinical Finding, Ingredient, etc. No No
382 CONCEPT_CLASS concept_class_concept_id Yes integer A Concept that represents the Concept Class. No Yes CONCEPT CONCEPT_ID
383 CONCEPT_RELATIONSHIP concept_id_1 Yes integer No Yes CONCEPT CONCEPT_ID
384 CONCEPT_RELATIONSHIP concept_id_2 Yes integer No Yes CONCEPT CONCEPT_ID
385 CONCEPT_RELATIONSHIP relationship_id Yes varchar(20) The relationship between CONCEPT_ID_1 and CONCEPT_ID_2. Please see the [Vocabulary Conventions](https://ohdsi.github.io/CommonDataModel/dataModelConventions.html#concept_relationships). for more information. No Yes RELATIONSHIP RELATIONSHIP_ID
386 CONCEPT_RELATIONSHIP valid_start_date Yes date The date when the relationship is first recorded. No No
387 CONCEPT_RELATIONSHIP valid_end_date Yes date The date when the relationship is invalidated. No No
401 CONCEPT_ANCESTOR max_levels_of_separation Yes integer The maximum separation in number of levels of hierarchy between ancestor and descendant concepts. This is an attribute that is used to simplify hierarchic analysis. No No
402 SOURCE_TO_CONCEPT_MAP source_code Yes varchar(50) The source code being translated into a Standard Concept. No No
403 SOURCE_TO_CONCEPT_MAP source_concept_id Yes integer A foreign key to the Source Concept that is being translated into a Standard Concept. This is either 0 or should be a number above 2 billion, which are the Concepts reserved for site-specific codes and mappings. No Yes CONCEPT CONCEPT_ID
404 SOURCE_TO_CONCEPT_MAP source_vocabulary_id Yes varchar(20) A foreign key to the VOCABULARY table defining the vocabulary of the source code that is being translated to a Standard Concept. No No
405 SOURCE_TO_CONCEPT_MAP source_code_description No varchar(255) An optional description for the source code. This is included as a convenience to compare the description of the source code to the name of the concept. No No
406 SOURCE_TO_CONCEPT_MAP target_concept_id Yes integer The target Concept to which the source code is being mapped. No Yes CONCEPT CONCEPT_ID
407 SOURCE_TO_CONCEPT_MAP target_vocabulary_id Yes varchar(20) The Vocabulary of the target Concept. No Yes VOCABULARY VOCABULARY_ID
408 SOURCE_TO_CONCEPT_MAP valid_start_date Yes date The date when the mapping instance was first recorded. No No

12
inst/ddl/5.3/bigquery/OMOPCDM_bigquery_5.3_ddl.sql
View File

@ -351,8 +351,8 @@ create table @cdmDatabaseSchema.drug_era (
drug_era_id INT64 not null,
person_id INT64 not null,
drug_concept_id INT64 not null,
drug_era_start_date datetime not null,
drug_era_end_date datetime not null,
drug_era_start_date date not null,
drug_era_end_date date not null,
drug_exposure_count INT64,
gap_days INT64 );
@ -363,16 +363,16 @@ create table @cdmDatabaseSchema.dose_era (
drug_concept_id INT64 not null,
unit_concept_id INT64 not null,
dose_value FLOAT64 not null,
dose_era_start_date datetime not null,
dose_era_end_date datetime not null );
dose_era_start_date date not null,
dose_era_end_date date not null );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.condition_era (
condition_era_id INT64 not null,
person_id INT64 not null,
condition_concept_id INT64 not null,
condition_era_start_date datetime not null,
condition_era_end_date datetime not null,
condition_era_start_date date not null,
condition_era_end_date date not null,
condition_occurrence_count INT64 );
--HINT DISTRIBUTE ON RANDOM

12
inst/ddl/5.3/netezza/OMOPCDM_netezza_5.3_ddl.sql
View File

@ -351,8 +351,8 @@ CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date TIMESTAMP NOT NULL,
drug_era_end_date TIMESTAMP NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL );
@ -363,16 +363,16 @@ CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value FLOAT(6) NOT NULL,
dose_era_start_date TIMESTAMP NOT NULL,
dose_era_end_date TIMESTAMP NOT NULL );
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date TIMESTAMP NOT NULL,
condition_era_end_date TIMESTAMP NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL );
--HINT DISTRIBUTE ON RANDOM

12
inst/ddl/5.3/oracle/OMOPCDM_oracle_5.3_ddl.sql
View File

@ -351,8 +351,8 @@ CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date TIMESTAMP NOT NULL,
drug_era_end_date TIMESTAMP NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL );
@ -363,16 +363,16 @@ CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value float NOT NULL,
dose_era_start_date TIMESTAMP NOT NULL,
dose_era_end_date TIMESTAMP NOT NULL );
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date TIMESTAMP NOT NULL,
condition_era_end_date TIMESTAMP NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL );
--HINT DISTRIBUTE ON RANDOM

12
inst/ddl/5.3/pdw/OMOPCDM_pdw_5.3_ddl.sql
View File

@ -350,8 +350,8 @@ WITH (DISTRIBUTION = REPLICATE);
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date datetime NOT NULL,
drug_era_end_date datetime NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL )
WITH (DISTRIBUTION = HASH(person_id));
@ -362,16 +362,16 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (dose_era
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value float NOT NULL,
dose_era_start_date datetime NOT NULL,
dose_era_end_date datetime NOT NULL )
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL )
WITH (DISTRIBUTION = HASH(person_id));
--HINT DISTRIBUTE ON KEY (person_id)
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date datetime NOT NULL,
condition_era_end_date datetime NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL )
WITH (DISTRIBUTION = HASH(person_id));

12
inst/ddl/5.3/postgresql/OMOPCDM_postgresql_5.3_ddl.sql
View File

@ -351,8 +351,8 @@ CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date TIMESTAMP NOT NULL,
drug_era_end_date TIMESTAMP NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL );
@ -363,16 +363,16 @@ CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value NUMERIC NOT NULL,
dose_era_start_date TIMESTAMP NOT NULL,
dose_era_end_date TIMESTAMP NOT NULL );
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date TIMESTAMP NOT NULL,
condition_era_end_date TIMESTAMP NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL );
--HINT DISTRIBUTE ON RANDOM

12
inst/ddl/5.3/redshift/OMOPCDM_redshift_5.3_ddl.sql
View File

@ -350,8 +350,8 @@ DISTSTYLE ALL;
CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date TIMESTAMP NOT NULL,
drug_era_end_date TIMESTAMP NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL )
DISTKEY(person_id);
@ -362,16 +362,16 @@ CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (dose_era_id integer NOT NULL,
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value float NOT NULL,
dose_era_start_date TIMESTAMP NOT NULL,
dose_era_end_date TIMESTAMP NOT NULL )
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL )
DISTKEY(person_id);
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date TIMESTAMP NOT NULL,
condition_era_end_date TIMESTAMP NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL )
DISTKEY(person_id);

158
inst/ddl/5.3/spark/OMOPCDM_spark_5.3_constraints.sql Normal file
View File

@ -0,0 +1,158 @@
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_gender_concept_id FOREIGN KEY (gender_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_race_concept_id FOREIGN KEY (race_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_ethnicity_concept_id FOREIGN KEY (ethnicity_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_location_id FOREIGN KEY (location_id) REFERENCES @cdmDatabaseSchema.LOCATION (LOCATION_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_gender_source_concept_id FOREIGN KEY (gender_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_race_source_concept_id FOREIGN KEY (race_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_ethnicity_source_concept_id FOREIGN KEY (ethnicity_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD ADD CONSTRAINT fpk_OBSERVATION_PERIOD_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD ADD CONSTRAINT fpk_OBSERVATION_PERIOD_period_type_concept_id FOREIGN KEY (period_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_visit_concept_id FOREIGN KEY (visit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_visit_type_concept_id FOREIGN KEY (visit_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_visit_source_concept_id FOREIGN KEY (visit_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_admitting_source_concept_id FOREIGN KEY (admitting_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_discharge_to_concept_id FOREIGN KEY (discharge_to_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_preceding_visit_occurrence_id FOREIGN KEY (preceding_visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_detail_concept_id FOREIGN KEY (visit_detail_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_detail_type_concept_id FOREIGN KEY (visit_detail_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_detail_source_concept_id FOREIGN KEY (visit_detail_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_admitting_source_concept_id FOREIGN KEY (admitting_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_discharge_to_concept_id FOREIGN KEY (discharge_to_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_preceding_visit_detail_id FOREIGN KEY (preceding_visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_detail_parent_id FOREIGN KEY (visit_detail_parent_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_concept_id FOREIGN KEY (condition_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_type_concept_id FOREIGN KEY (condition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_status_concept_id FOREIGN KEY (condition_status_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_source_concept_id FOREIGN KEY (condition_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_drug_type_concept_id FOREIGN KEY (drug_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_route_concept_id FOREIGN KEY (route_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_drug_source_concept_id FOREIGN KEY (drug_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_procedure_concept_id FOREIGN KEY (procedure_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_procedure_type_concept_id FOREIGN KEY (procedure_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_modifier_concept_id FOREIGN KEY (modifier_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_device_concept_id FOREIGN KEY (device_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_device_type_concept_id FOREIGN KEY (device_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_device_source_concept_id FOREIGN KEY (device_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_measurement_concept_id FOREIGN KEY (measurement_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_measurement_type_concept_id FOREIGN KEY (measurement_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_operator_concept_id FOREIGN KEY (operator_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_value_as_concept_id FOREIGN KEY (value_as_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_measurement_source_concept_id FOREIGN KEY (measurement_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_observation_concept_id FOREIGN KEY (observation_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_observation_type_concept_id FOREIGN KEY (observation_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_value_as_concept_id FOREIGN KEY (value_as_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_qualifier_concept_id FOREIGN KEY (qualifier_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_observation_source_concept_id FOREIGN KEY (observation_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_death_type_concept_id FOREIGN KEY (death_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_cause_concept_id FOREIGN KEY (cause_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_cause_source_concept_id FOREIGN KEY (cause_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_note_type_concept_id FOREIGN KEY (note_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_note_class_concept_id FOREIGN KEY (note_class_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_encoding_concept_id FOREIGN KEY (encoding_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_language_concept_id FOREIGN KEY (language_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT fpk_NOTE_NLP_section_concept_id FOREIGN KEY (section_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT fpk_NOTE_NLP_note_nlp_concept_id FOREIGN KEY (note_nlp_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT fpk_NOTE_NLP_note_nlp_source_concept_id FOREIGN KEY (note_nlp_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_specimen_concept_id FOREIGN KEY (specimen_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_specimen_type_concept_id FOREIGN KEY (specimen_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_anatomic_site_concept_id FOREIGN KEY (anatomic_site_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_disease_status_concept_id FOREIGN KEY (disease_status_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP ADD CONSTRAINT fpk_FACT_RELATIONSHIP_domain_concept_id_1 FOREIGN KEY (domain_concept_id_1) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP ADD CONSTRAINT fpk_FACT_RELATIONSHIP_domain_concept_id_2 FOREIGN KEY (domain_concept_id_2) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP ADD CONSTRAINT fpk_FACT_RELATIONSHIP_relationship_concept_id FOREIGN KEY (relationship_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CARE_SITE ADD CONSTRAINT fpk_CARE_SITE_place_of_service_concept_id FOREIGN KEY (place_of_service_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CARE_SITE ADD CONSTRAINT fpk_CARE_SITE_location_id FOREIGN KEY (location_id) REFERENCES @cdmDatabaseSchema.LOCATION (LOCATION_ID);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_specialty_concept_id FOREIGN KEY (specialty_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_gender_concept_id FOREIGN KEY (gender_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_specialty_source_concept_id FOREIGN KEY (specialty_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_gender_source_concept_id FOREIGN KEY (gender_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_payer_plan_period_id FOREIGN KEY (payer_plan_period_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_payer_concept_id FOREIGN KEY (payer_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_payer_source_concept_id FOREIGN KEY (payer_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_plan_concept_id FOREIGN KEY (plan_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_plan_source_concept_id FOREIGN KEY (plan_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_sponsor_concept_id FOREIGN KEY (sponsor_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_sponsor_source_concept_id FOREIGN KEY (sponsor_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_stop_reason_concept_id FOREIGN KEY (stop_reason_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_stop_reason_source_concept_id FOREIGN KEY (stop_reason_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_cost_domain_id FOREIGN KEY (cost_domain_id) REFERENCES @cdmDatabaseSchema.DOMAIN (DOMAIN_ID);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_cost_type_concept_id FOREIGN KEY (cost_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_currency_concept_id FOREIGN KEY (currency_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_revenue_code_concept_id FOREIGN KEY (revenue_code_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_drg_concept_id FOREIGN KEY (drg_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_ERA ADD CONSTRAINT fpk_DRUG_ERA_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_ERA ADD CONSTRAINT fpk_DRUG_ERA_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT fpk_DOSE_ERA_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT fpk_DOSE_ERA_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT fpk_DOSE_ERA_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_condition_concept_id FOREIGN KEY (condition_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT fpk_METADATA_metadata_concept_id FOREIGN KEY (metadata_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT fpk_METADATA_metadata_type_concept_id FOREIGN KEY (metadata_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT fpk_METADATA_value_as_concept_id FOREIGN KEY (value_as_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT fpk_CONCEPT_domain_id FOREIGN KEY (domain_id) REFERENCES @cdmDatabaseSchema.DOMAIN (DOMAIN_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT fpk_CONCEPT_vocabulary_id FOREIGN KEY (vocabulary_id) REFERENCES @cdmDatabaseSchema.VOCABULARY (VOCABULARY_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT fpk_CONCEPT_concept_class_id FOREIGN KEY (concept_class_id) REFERENCES @cdmDatabaseSchema.CONCEPT_CLASS (CONCEPT_CLASS_ID);
ALTER TABLE @cdmDatabaseSchema.VOCABULARY ADD CONSTRAINT fpk_VOCABULARY_vocabulary_concept_id FOREIGN KEY (vocabulary_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DOMAIN ADD CONSTRAINT fpk_DOMAIN_domain_concept_id FOREIGN KEY (domain_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_CLASS ADD CONSTRAINT fpk_CONCEPT_CLASS_concept_class_concept_id FOREIGN KEY (concept_class_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP ADD CONSTRAINT fpk_CONCEPT_RELATIONSHIP_concept_id_1 FOREIGN KEY (concept_id_1) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP ADD CONSTRAINT fpk_CONCEPT_RELATIONSHIP_concept_id_2 FOREIGN KEY (concept_id_2) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP ADD CONSTRAINT fpk_CONCEPT_RELATIONSHIP_relationship_id FOREIGN KEY (relationship_id) REFERENCES @cdmDatabaseSchema.RELATIONSHIP (RELATIONSHIP_ID);
ALTER TABLE @cdmDatabaseSchema.RELATIONSHIP ADD CONSTRAINT fpk_RELATIONSHIP_relationship_concept_id FOREIGN KEY (relationship_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM ADD CONSTRAINT fpk_CONCEPT_SYNONYM_concept_id FOREIGN KEY (concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM ADD CONSTRAINT fpk_CONCEPT_SYNONYM_language_concept_id FOREIGN KEY (language_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR ADD CONSTRAINT fpk_CONCEPT_ANCESTOR_ancestor_concept_id FOREIGN KEY (ancestor_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR ADD CONSTRAINT fpk_CONCEPT_ANCESTOR_descendant_concept_id FOREIGN KEY (descendant_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP ADD CONSTRAINT fpk_SOURCE_TO_CONCEPT_MAP_source_concept_id FOREIGN KEY (source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP ADD CONSTRAINT fpk_SOURCE_TO_CONCEPT_MAP_target_concept_id FOREIGN KEY (target_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP ADD CONSTRAINT fpk_SOURCE_TO_CONCEPT_MAP_target_vocabulary_id FOREIGN KEY (target_vocabulary_id) REFERENCES @cdmDatabaseSchema.VOCABULARY (VOCABULARY_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_ingredient_concept_id FOREIGN KEY (ingredient_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_amount_unit_concept_id FOREIGN KEY (amount_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_numerator_unit_concept_id FOREIGN KEY (numerator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_denominator_unit_concept_id FOREIGN KEY (denominator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_definition_type_concept_id FOREIGN KEY (definition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_subject_concept_id FOREIGN KEY (subject_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.ATTRIBUTE_DEFINITION ADD CONSTRAINT fpk_ATTRIBUTE_DEFINITION_attribute_type_concept_id FOREIGN KEY (attribute_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

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--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.PERSON
USING DELTA
AS
SELECT CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS gender_concept_id,
CAST(NULL AS integer) AS year_of_birth,
CAST(NULL AS integer) AS month_of_birth,
CAST(NULL AS integer) AS day_of_birth,
CAST(NULL AS TIMESTAMP) AS birth_datetime,
CAST(NULL AS integer) AS race_concept_id,
CAST(NULL AS integer) AS ethnicity_concept_id,
CAST(NULL AS integer) AS location_id,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS care_site_id,
CAST(NULL AS STRING) AS person_source_value,
CAST(NULL AS STRING) AS gender_source_value,
CAST(NULL AS integer) AS gender_source_concept_id,
CAST(NULL AS STRING) AS race_source_value,
CAST(NULL AS integer) AS race_source_concept_id,
CAST(NULL AS STRING) AS ethnicity_source_value,
CAST(NULL AS integer) AS ethnicity_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD
USING DELTA
AS
SELECT CAST(NULL AS integer) AS observation_period_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS date) AS observation_period_start_date,
CAST(NULL AS date) AS observation_period_end_date,
CAST(NULL AS integer) AS period_type_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS visit_concept_id,
CAST(NULL AS date) AS visit_start_date,
CAST(NULL AS TIMESTAMP) AS visit_start_datetime,
CAST(NULL AS date) AS visit_end_date,
CAST(NULL AS TIMESTAMP) AS visit_end_datetime,
CAST(NULL AS integer) AS visit_type_concept_id,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS care_site_id,
CAST(NULL AS STRING) AS visit_source_value,
CAST(NULL AS integer) AS visit_source_concept_id,
CAST(NULL AS integer) AS admitting_source_concept_id,
CAST(NULL AS STRING) AS admitting_source_value,
CAST(NULL AS integer) AS discharge_to_concept_id,
CAST(NULL AS STRING) AS discharge_to_source_value,
CAST(NULL AS integer) AS preceding_visit_occurrence_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.VISIT_DETAIL
USING DELTA
AS
SELECT CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS visit_detail_concept_id,
CAST(NULL AS date) AS visit_detail_start_date,
CAST(NULL AS TIMESTAMP) AS visit_detail_start_datetime,
CAST(NULL AS date) AS visit_detail_end_date,
CAST(NULL AS TIMESTAMP) AS visit_detail_end_datetime,
CAST(NULL AS integer) AS visit_detail_type_concept_id,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS care_site_id,
CAST(NULL AS STRING) AS visit_detail_source_value,
CAST(NULL AS integer) AS visit_detail_source_concept_id,
CAST(NULL AS STRING) AS admitting_source_value,
CAST(NULL AS integer) AS admitting_source_concept_id,
CAST(NULL AS STRING) AS discharge_to_source_value,
CAST(NULL AS integer) AS discharge_to_concept_id,
CAST(NULL AS integer) AS preceding_visit_detail_id,
CAST(NULL AS integer) AS visit_detail_parent_id,
CAST(NULL AS integer) AS visit_occurrence_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS condition_occurrence_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS condition_concept_id,
CAST(NULL AS date) AS condition_start_date,
CAST(NULL AS TIMESTAMP) AS condition_start_datetime,
CAST(NULL AS date) AS condition_end_date,
CAST(NULL AS TIMESTAMP) AS condition_end_datetime,
CAST(NULL AS integer) AS condition_type_concept_id,
CAST(NULL AS integer) AS condition_status_concept_id,
CAST(NULL AS STRING) AS stop_reason,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS condition_source_value,
CAST(NULL AS integer) AS condition_source_concept_id,
CAST(NULL AS STRING) AS condition_status_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DRUG_EXPOSURE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS drug_exposure_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS drug_concept_id,
CAST(NULL AS date) AS drug_exposure_start_date,
CAST(NULL AS TIMESTAMP) AS drug_exposure_start_datetime,
CAST(NULL AS date) AS drug_exposure_end_date,
CAST(NULL AS TIMESTAMP) AS drug_exposure_end_datetime,
CAST(NULL AS date) AS verbatim_end_date,
CAST(NULL AS integer) AS drug_type_concept_id,
CAST(NULL AS STRING) AS stop_reason,
CAST(NULL AS integer) AS refills,
CAST(NULL AS float) AS quantity,
CAST(NULL AS integer) AS days_supply,
CAST(NULL AS STRING) AS sig,
CAST(NULL AS integer) AS route_concept_id,
CAST(NULL AS STRING) AS lot_number,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS drug_source_value,
CAST(NULL AS integer) AS drug_source_concept_id,
CAST(NULL AS STRING) AS route_source_value,
CAST(NULL AS STRING) AS dose_unit_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS procedure_occurrence_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS procedure_concept_id,
CAST(NULL AS date) AS procedure_date,
CAST(NULL AS TIMESTAMP) AS procedure_datetime,
CAST(NULL AS integer) AS procedure_type_concept_id,
CAST(NULL AS integer) AS modifier_concept_id,
CAST(NULL AS integer) AS quantity,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS procedure_source_value,
CAST(NULL AS integer) AS procedure_source_concept_id,
CAST(NULL AS STRING) AS modifier_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS device_exposure_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS device_concept_id,
CAST(NULL AS date) AS device_exposure_start_date,
CAST(NULL AS TIMESTAMP) AS device_exposure_start_datetime,
CAST(NULL AS date) AS device_exposure_end_date,
CAST(NULL AS TIMESTAMP) AS device_exposure_end_datetime,
CAST(NULL AS integer) AS device_type_concept_id,
CAST(NULL AS STRING) AS unique_device_id,
CAST(NULL AS integer) AS quantity,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS device_source_value,
CAST(NULL AS integer) AS device_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.MEASUREMENT
USING DELTA
AS
SELECT CAST(NULL AS integer) AS measurement_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS measurement_concept_id,
CAST(NULL AS date) AS measurement_date,
CAST(NULL AS TIMESTAMP) AS measurement_datetime,
CAST(NULL AS STRING) AS measurement_time,
CAST(NULL AS integer) AS measurement_type_concept_id,
CAST(NULL AS integer) AS operator_concept_id,
CAST(NULL AS float) AS value_as_number,
CAST(NULL AS integer) AS value_as_concept_id,
CAST(NULL AS integer) AS unit_concept_id,
CAST(NULL AS float) AS range_low,
CAST(NULL AS float) AS range_high,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS measurement_source_value,
CAST(NULL AS integer) AS measurement_source_concept_id,
CAST(NULL AS STRING) AS unit_source_value,
CAST(NULL AS STRING) AS value_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.OBSERVATION
USING DELTA
AS
SELECT CAST(NULL AS integer) AS observation_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS observation_concept_id,
CAST(NULL AS date) AS observation_date,
CAST(NULL AS TIMESTAMP) AS observation_datetime,
CAST(NULL AS integer) AS observation_type_concept_id,
CAST(NULL AS float) AS value_as_number,
CAST(NULL AS STRING) AS value_as_string,
CAST(NULL AS integer) AS value_as_concept_id,
CAST(NULL AS integer) AS qualifier_concept_id,
CAST(NULL AS integer) AS unit_concept_id,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS observation_source_value,
CAST(NULL AS integer) AS observation_source_concept_id,
CAST(NULL AS STRING) AS unit_source_value,
CAST(NULL AS STRING) AS qualifier_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DEATH
USING DELTA
AS
SELECT CAST(NULL AS integer) AS person_id,
CAST(NULL AS date) AS death_date,
CAST(NULL AS TIMESTAMP) AS death_datetime,
CAST(NULL AS integer) AS death_type_concept_id,
CAST(NULL AS integer) AS cause_concept_id,
CAST(NULL AS STRING) AS cause_source_value,
CAST(NULL AS integer) AS cause_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.NOTE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS note_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS date) AS note_date,
CAST(NULL AS TIMESTAMP) AS note_datetime,
CAST(NULL AS integer) AS note_type_concept_id,
CAST(NULL AS integer) AS note_class_concept_id,
CAST(NULL AS STRING) AS note_title,
CAST(NULL AS STRING) AS note_text,
CAST(NULL AS integer) AS encoding_concept_id,
CAST(NULL AS integer) AS language_concept_id,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS note_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.NOTE_NLP
USING DELTA
AS
SELECT CAST(NULL AS integer) AS note_nlp_id,
CAST(NULL AS integer) AS note_id,
CAST(NULL AS integer) AS section_concept_id,
CAST(NULL AS STRING) AS snippet,
CAST(NULL AS STRING) AS offset,
CAST(NULL AS STRING) AS lexical_variant,
CAST(NULL AS integer) AS note_nlp_concept_id,
CAST(NULL AS integer) AS note_nlp_source_concept_id,
CAST(NULL AS STRING) AS nlp_system,
CAST(NULL AS date) AS nlp_date,
CAST(NULL AS TIMESTAMP) AS nlp_datetime,
CAST(NULL AS STRING) AS term_exists,
CAST(NULL AS STRING) AS term_temporal,
CAST(NULL AS STRING) AS term_modifiers WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.SPECIMEN
USING DELTA
AS
SELECT CAST(NULL AS integer) AS specimen_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS specimen_concept_id,
CAST(NULL AS integer) AS specimen_type_concept_id,
CAST(NULL AS date) AS specimen_date,
CAST(NULL AS TIMESTAMP) AS specimen_datetime,
CAST(NULL AS float) AS quantity,
CAST(NULL AS integer) AS unit_concept_id,
CAST(NULL AS integer) AS anatomic_site_concept_id,
CAST(NULL AS integer) AS disease_status_concept_id,
CAST(NULL AS STRING) AS specimen_source_id,
CAST(NULL AS STRING) AS specimen_source_value,
CAST(NULL AS STRING) AS unit_source_value,
CAST(NULL AS STRING) AS anatomic_site_source_value,
CAST(NULL AS STRING) AS disease_status_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP
USING DELTA
AS
SELECT CAST(NULL AS integer) AS domain_concept_id_1,
CAST(NULL AS integer) AS fact_id_1,
CAST(NULL AS integer) AS domain_concept_id_2,
CAST(NULL AS integer) AS fact_id_2,
CAST(NULL AS integer) AS relationship_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.LOCATION
USING DELTA
AS
SELECT CAST(NULL AS integer) AS location_id,
CAST(NULL AS STRING) AS address_1,
CAST(NULL AS STRING) AS address_2,
CAST(NULL AS STRING) AS city,
CAST(NULL AS STRING) AS state,
CAST(NULL AS STRING) AS zip,
CAST(NULL AS STRING) AS county,
CAST(NULL AS STRING) AS location_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CARE_SITE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS care_site_id,
CAST(NULL AS STRING) AS care_site_name,
CAST(NULL AS integer) AS place_of_service_concept_id,
CAST(NULL AS integer) AS location_id,
CAST(NULL AS STRING) AS care_site_source_value,
CAST(NULL AS STRING) AS place_of_service_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.PROVIDER
USING DELTA
AS
SELECT CAST(NULL AS integer) AS provider_id,
CAST(NULL AS STRING) AS provider_name,
CAST(NULL AS STRING) AS npi,
CAST(NULL AS STRING) AS dea,
CAST(NULL AS integer) AS specialty_concept_id,
CAST(NULL AS integer) AS care_site_id,
CAST(NULL AS integer) AS year_of_birth,
CAST(NULL AS integer) AS gender_concept_id,
CAST(NULL AS STRING) AS provider_source_value,
CAST(NULL AS STRING) AS specialty_source_value,
CAST(NULL AS integer) AS specialty_source_concept_id,
CAST(NULL AS STRING) AS gender_source_value,
CAST(NULL AS integer) AS gender_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD
USING DELTA
AS
SELECT CAST(NULL AS integer) AS payer_plan_period_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS date) AS payer_plan_period_start_date,
CAST(NULL AS date) AS payer_plan_period_end_date,
CAST(NULL AS integer) AS payer_concept_id,
CAST(NULL AS STRING) AS payer_source_value,
CAST(NULL AS integer) AS payer_source_concept_id,
CAST(NULL AS integer) AS plan_concept_id,
CAST(NULL AS STRING) AS plan_source_value,
CAST(NULL AS integer) AS plan_source_concept_id,
CAST(NULL AS integer) AS sponsor_concept_id,
CAST(NULL AS STRING) AS sponsor_source_value,
CAST(NULL AS integer) AS sponsor_source_concept_id,
CAST(NULL AS STRING) AS family_source_value,
CAST(NULL AS integer) AS stop_reason_concept_id,
CAST(NULL AS STRING) AS stop_reason_source_value,
CAST(NULL AS integer) AS stop_reason_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.COST
USING DELTA
AS
SELECT CAST(NULL AS integer) AS cost_id,
CAST(NULL AS integer) AS cost_event_id,
CAST(NULL AS STRING) AS cost_domain_id,
CAST(NULL AS integer) AS cost_type_concept_id,
CAST(NULL AS integer) AS currency_concept_id,
CAST(NULL AS float) AS total_charge,
CAST(NULL AS float) AS total_cost,
CAST(NULL AS float) AS total_paid,
CAST(NULL AS float) AS paid_by_payer,
CAST(NULL AS float) AS paid_by_patient,
CAST(NULL AS float) AS paid_patient_copay,
CAST(NULL AS float) AS paid_patient_coinsurance,
CAST(NULL AS float) AS paid_patient_deductible,
CAST(NULL AS float) AS paid_by_primary,
CAST(NULL AS float) AS paid_ingredient_cost,
CAST(NULL AS float) AS paid_dispensing_fee,
CAST(NULL AS integer) AS payer_plan_period_id,
CAST(NULL AS float) AS amount_allowed,
CAST(NULL AS integer) AS revenue_code_concept_id,
CAST(NULL AS STRING) AS revenue_code_source_value,
CAST(NULL AS integer) AS drg_concept_id,
CAST(NULL AS STRING) AS drg_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DRUG_ERA
USING DELTA
AS
SELECT CAST(NULL AS integer) AS drug_era_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS drug_concept_id,
CAST(NULL AS date) AS drug_era_start_date,
CAST(NULL AS date) AS drug_era_end_date,
CAST(NULL AS integer) AS drug_exposure_count,
CAST(NULL AS integer) AS gap_days WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DOSE_ERA
USING DELTA
AS
SELECT CAST(NULL AS integer) AS dose_era_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS drug_concept_id,
CAST(NULL AS integer) AS unit_concept_id,
CAST(NULL AS float) AS dose_value,
CAST(NULL AS date) AS dose_era_start_date,
CAST(NULL AS date) AS dose_era_end_date WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA
USING DELTA
AS
SELECT CAST(NULL AS integer) AS condition_era_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS condition_concept_id,
CAST(NULL AS date) AS condition_era_start_date,
CAST(NULL AS date) AS condition_era_end_date,
CAST(NULL AS integer) AS condition_occurrence_count WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.METADATA
USING DELTA
AS
SELECT CAST(NULL AS integer) AS metadata_concept_id,
CAST(NULL AS integer) AS metadata_type_concept_id,
CAST(NULL AS STRING) AS name,
CAST(NULL AS STRING) AS value_as_string,
CAST(NULL AS integer) AS value_as_concept_id,
CAST(NULL AS date) AS metadata_date,
CAST(NULL AS TIMESTAMP) AS metadata_datetime WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CDM_SOURCE
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS cdm_source_name,
CAST(NULL AS STRING) AS cdm_source_abbreviation,
CAST(NULL AS STRING) AS cdm_holder,
CAST(NULL AS STRING) AS source_description,
CAST(NULL AS STRING) AS source_documentation_reference,
CAST(NULL AS STRING) AS cdm_etl_reference,
CAST(NULL AS date) AS source_release_date,
CAST(NULL AS date) AS cdm_release_date,
CAST(NULL AS STRING) AS cdm_version,
CAST(NULL AS STRING) AS vocabulary_version WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT
USING DELTA
AS
SELECT CAST(NULL AS integer) AS concept_id,
CAST(NULL AS STRING) AS concept_name,
CAST(NULL AS STRING) AS domain_id,
CAST(NULL AS STRING) AS vocabulary_id,
CAST(NULL AS STRING) AS concept_class_id,
CAST(NULL AS STRING) AS standard_concept,
CAST(NULL AS STRING) AS concept_code,
CAST(NULL AS date) AS valid_start_date,
CAST(NULL AS date) AS valid_end_date,
CAST(NULL AS STRING) AS invalid_reason WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.VOCABULARY
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS vocabulary_id,
CAST(NULL AS STRING) AS vocabulary_name,
CAST(NULL AS STRING) AS vocabulary_reference,
CAST(NULL AS STRING) AS vocabulary_version,
CAST(NULL AS integer) AS vocabulary_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.DOMAIN
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS domain_id,
CAST(NULL AS STRING) AS domain_name,
CAST(NULL AS integer) AS domain_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT_CLASS
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS concept_class_id,
CAST(NULL AS STRING) AS concept_class_name,
CAST(NULL AS integer) AS concept_class_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP
USING DELTA
AS
SELECT CAST(NULL AS integer) AS concept_id_1,
CAST(NULL AS integer) AS concept_id_2,
CAST(NULL AS STRING) AS relationship_id,
CAST(NULL AS date) AS valid_start_date,
CAST(NULL AS date) AS valid_end_date,
CAST(NULL AS STRING) AS invalid_reason WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.RELATIONSHIP
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS relationship_id,
CAST(NULL AS STRING) AS relationship_name,
CAST(NULL AS STRING) AS is_hierarchical,
CAST(NULL AS STRING) AS defines_ancestry,
CAST(NULL AS STRING) AS reverse_relationship_id,
CAST(NULL AS integer) AS relationship_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM
USING DELTA
AS
SELECT CAST(NULL AS integer) AS concept_id,
CAST(NULL AS STRING) AS concept_synonym_name,
CAST(NULL AS integer) AS language_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR
USING DELTA
AS
SELECT CAST(NULL AS integer) AS ancestor_concept_id,
CAST(NULL AS integer) AS descendant_concept_id,
CAST(NULL AS integer) AS min_levels_of_separation,
CAST(NULL AS integer) AS max_levels_of_separation WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS source_code,
CAST(NULL AS integer) AS source_concept_id,
CAST(NULL AS STRING) AS source_vocabulary_id,
CAST(NULL AS STRING) AS source_code_description,
CAST(NULL AS integer) AS target_concept_id,
CAST(NULL AS STRING) AS target_vocabulary_id,
CAST(NULL AS date) AS valid_start_date,
CAST(NULL AS date) AS valid_end_date,
CAST(NULL AS STRING) AS invalid_reason WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.DRUG_STRENGTH
USING DELTA
AS
SELECT CAST(NULL AS integer) AS drug_concept_id,
CAST(NULL AS integer) AS ingredient_concept_id,
CAST(NULL AS float) AS amount_value,
CAST(NULL AS integer) AS amount_unit_concept_id,
CAST(NULL AS float) AS numerator_value,
CAST(NULL AS integer) AS numerator_unit_concept_id,
CAST(NULL AS float) AS denominator_value,
CAST(NULL AS integer) AS denominator_unit_concept_id,
CAST(NULL AS integer) AS box_size,
CAST(NULL AS date) AS valid_start_date,
CAST(NULL AS date) AS valid_end_date,
CAST(NULL AS STRING) AS invalid_reason WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.COHORT_DEFINITION
USING DELTA
AS
SELECT CAST(NULL AS integer) AS cohort_definition_id,
CAST(NULL AS STRING) AS cohort_definition_name,
CAST(NULL AS STRING) AS cohort_definition_description,
CAST(NULL AS integer) AS definition_type_concept_id,
CAST(NULL AS STRING) AS cohort_definition_syntax,
CAST(NULL AS integer) AS subject_concept_id,
CAST(NULL AS date) AS cohort_initiation_date WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.ATTRIBUTE_DEFINITION
USING DELTA
AS
SELECT CAST(NULL AS integer) AS attribute_definition_id,
CAST(NULL AS STRING) AS attribute_name,
CAST(NULL AS STRING) AS attribute_description,
CAST(NULL AS integer) AS attribute_type_concept_id,
CAST(NULL AS STRING) AS attribute_syntax WHERE 1 = 0;

70
inst/ddl/5.3/spark/OMOPCDM_spark_5.3_indices.sql Normal file
View File

@ -0,0 +1,70 @@
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes

26
inst/ddl/5.3/spark/OMOPCDM_spark_5.3_primary_keys.sql Normal file
View File

@ -0,0 +1,26 @@
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT xpk_PERSON (person_id);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD ADD CONSTRAINT xpk_OBSERVATION_PERIOD (observation_period_id);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT xpk_VISIT_OCCURRENCE (visit_occurrence_id);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT xpk_VISIT_DETAIL (visit_detail_id);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT xpk_CONDITION_OCCURRENCE (condition_occurrence_id);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT xpk_DRUG_EXPOSURE (drug_exposure_id);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT xpk_PROCEDURE_OCCURRENCE (procedure_occurrence_id);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT xpk_DEVICE_EXPOSURE (device_exposure_id);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT xpk_MEASUREMENT (measurement_id);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT xpk_OBSERVATION (observation_id);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT xpk_NOTE (note_id);
ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT xpk_NOTE_NLP (note_nlp_id);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT xpk_SPECIMEN (specimen_id);
ALTER TABLE @cdmDatabaseSchema.LOCATION ADD CONSTRAINT xpk_LOCATION (location_id);
ALTER TABLE @cdmDatabaseSchema.CARE_SITE ADD CONSTRAINT xpk_CARE_SITE (care_site_id);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT xpk_PROVIDER (provider_id);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT xpk_PAYER_PLAN_PERIOD (payer_plan_period_id);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT xpk_COST (cost_id);
ALTER TABLE @cdmDatabaseSchema.DRUG_ERA ADD CONSTRAINT xpk_DRUG_ERA (drug_era_id);
ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT xpk_DOSE_ERA (dose_era_id);
ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT xpk_CONDITION_ERA (condition_era_id);
ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT xpk_CONCEPT (concept_id);
ALTER TABLE @cdmDatabaseSchema.VOCABULARY ADD CONSTRAINT xpk_VOCABULARY (vocabulary_id);
ALTER TABLE @cdmDatabaseSchema.DOMAIN ADD CONSTRAINT xpk_DOMAIN (domain_id);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_CLASS ADD CONSTRAINT xpk_CONCEPT_CLASS (concept_class_id);
ALTER TABLE @cdmDatabaseSchema.RELATIONSHIP ADD CONSTRAINT xpk_RELATIONSHIP (relationship_id);

12
inst/ddl/5.3/sql_server/OMOPCDM_sql_server_5.3_ddl.sql
View File

@ -351,8 +351,8 @@ CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date datetime NOT NULL,
drug_era_end_date datetime NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL );
@ -363,16 +363,16 @@ CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value float NOT NULL,
dose_era_start_date datetime NOT NULL,
dose_era_end_date datetime NOT NULL );
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date datetime NOT NULL,
condition_era_end_date datetime NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL );
--HINT DISTRIBUTE ON RANDOM

2
inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_constraints.sql
View File

@ -350,8 +350,6 @@ alter table @cdmDatabaseSchema.drug_strength add constraint fpk_drug_strength_nu
alter table @cdmDatabaseSchema.drug_strength add constraint fpk_drug_strength_denominator_unit_concept_id foreign key (denominator_unit_concept_id) references @cdmDatabaseSchema.concept (concept_id);
alter table @cdmDatabaseSchema.cohort_definition add constraint fpk_cohort_definition_cohort_definition_id foreign key (cohort_definition_id) references @cdmDatabaseSchema.cohort (cohort_definition_id);
alter table @cdmDatabaseSchema.cohort_definition add constraint fpk_cohort_definition_definition_type_concept_id foreign key (definition_type_concept_id) references @cdmDatabaseSchema.concept (concept_id);
alter table @cdmDatabaseSchema.cohort_definition add constraint fpk_cohort_definition_subject_concept_id foreign key (subject_concept_id) references @cdmDatabaseSchema.concept (concept_id);

12
inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_ddl.sql
View File

@ -369,8 +369,8 @@ create table @cdmDatabaseSchema.drug_era (
drug_era_id INT64 not null,
person_id INT64 not null,
drug_concept_id INT64 not null,
drug_era_start_date datetime not null,
drug_era_end_date datetime not null,
drug_era_start_date date not null,
drug_era_end_date date not null,
drug_exposure_count INT64,
gap_days INT64 );
@ -381,16 +381,16 @@ create table @cdmDatabaseSchema.dose_era (
drug_concept_id INT64 not null,
unit_concept_id INT64 not null,
dose_value FLOAT64 not null,
dose_era_start_date datetime not null,
dose_era_end_date datetime not null );
dose_era_start_date date not null,
dose_era_end_date date not null );
--HINT DISTRIBUTE ON KEY (person_id)
create table @cdmDatabaseSchema.condition_era (
condition_era_id INT64 not null,
person_id INT64 not null,
condition_concept_id INT64 not null,
condition_era_start_date datetime not null,
condition_era_end_date datetime not null,
condition_era_start_date date not null,
condition_era_end_date date not null,
condition_occurrence_count INT64 );
--HINT DISTRIBUTE ON KEY (person_id)

2
inst/ddl/5.4/impala/OMOPCDM_impala_5.4_constraints.sql
View File

@ -350,8 +350,6 @@ ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_nu
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_denominator_unit_concept_id FOREIGN KEY (denominator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_cohort_definition_id FOREIGN KEY (cohort_definition_id) REFERENCES @cdmDatabaseSchema.COHORT (COHORT_DEFINITION_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_definition_type_concept_id FOREIGN KEY (definition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_subject_concept_id FOREIGN KEY (subject_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

16
inst/ddl/5.4/impala/OMOPCDM_impala_5.4_ddl.sql
View File

@ -180,7 +180,7 @@ CREATE TABLE @cdmDatabaseSchema.MEASUREMENT (
unit_source_value VARCHAR(50),
unit_source_concept_id integer NULL,
value_source_value VARCHAR(50),
measurement_event_id BIGINT,
measurement_event_id integer NULL,
meas_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
@ -204,7 +204,7 @@ CREATE TABLE @cdmDatabaseSchema.OBSERVATION (
unit_source_value VARCHAR(50),
qualifier_source_value VARCHAR(50),
value_source_value VARCHAR(50),
observation_event_id BIGINT,
observation_event_id integer NULL,
obs_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
@ -233,7 +233,7 @@ CREATE TABLE @cdmDatabaseSchema.NOTE (
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
note_source_value VARCHAR(50),
note_event_id BIGINT,
note_event_id integer NULL,
note_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON RANDOM
@ -395,14 +395,14 @@ CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id BIGINT,
person_id BIGINT,
episode_id INT,
person_id INT,
episode_concept_id INT,
episode_start_date TIMESTAMP,
episode_start_datetime TIMESTAMP,
episode_end_date TIMESTAMP,
episode_end_datetime TIMESTAMP,
episode_parent_id BIGINT,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id INT,
episode_type_concept_id INT,
@ -411,8 +411,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id BIGINT,
event_id BIGINT,
episode_id INT,
event_id INT,
episode_event_field_concept_id INT );
--HINT DISTRIBUTE ON RANDOM

2
inst/ddl/5.4/netezza/OMOPCDM_netezza_5.4_constraints.sql
View File

@ -350,8 +350,6 @@ ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_nu
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_denominator_unit_concept_id FOREIGN KEY (denominator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_cohort_definition_id FOREIGN KEY (cohort_definition_id) REFERENCES @cdmDatabaseSchema.COHORT (COHORT_DEFINITION_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_definition_type_concept_id FOREIGN KEY (definition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_subject_concept_id FOREIGN KEY (subject_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

28
inst/ddl/5.4/netezza/OMOPCDM_netezza_5.4_ddl.sql
View File

@ -180,7 +180,7 @@ CREATE TABLE @cdmDatabaseSchema.MEASUREMENT (
unit_source_value varchar(50) NULL,
unit_source_concept_id integer NULL,
value_source_value varchar(50) NULL,
measurement_event_id bigint NULL,
measurement_event_id integer NULL,
meas_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
@ -204,7 +204,7 @@ CREATE TABLE @cdmDatabaseSchema.OBSERVATION (
unit_source_value varchar(50) NULL,
qualifier_source_value varchar(50) NULL,
value_source_value varchar(50) NULL,
observation_event_id bigint NULL,
observation_event_id integer NULL,
obs_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
@ -233,7 +233,7 @@ CREATE TABLE @cdmDatabaseSchema.NOTE (
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
note_source_value varchar(50) NULL,
note_event_id bigint NULL,
note_event_id integer NULL,
note_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON RANDOM
@ -369,8 +369,8 @@ CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date TIMESTAMP NOT NULL,
drug_era_end_date TIMESTAMP NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL );
@ -381,28 +381,28 @@ CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value FLOAT(6) NOT NULL,
dose_era_start_date TIMESTAMP NOT NULL,
dose_era_end_date TIMESTAMP NOT NULL );
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date TIMESTAMP NOT NULL,
condition_era_end_date TIMESTAMP NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_id integer NOT NULL,
person_id integer NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime TIMESTAMP NULL,
episode_end_date date NULL,
episode_end_datetime TIMESTAMP NULL,
episode_parent_id bigint NULL,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -411,8 +411,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM

2
inst/ddl/5.4/oracle/OMOPCDM_oracle_5.4_constraints.sql
View File

@ -350,8 +350,6 @@ ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_nu
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_denominator_unit_concept_id FOREIGN KEY (denominator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_cohort_definition_id FOREIGN KEY (cohort_definition_id) REFERENCES @cdmDatabaseSchema.COHORT (COHORT_DEFINITION_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_definition_type_concept_id FOREIGN KEY (definition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_subject_concept_id FOREIGN KEY (subject_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

28
inst/ddl/5.4/oracle/OMOPCDM_oracle_5.4_ddl.sql
View File

@ -180,7 +180,7 @@ CREATE TABLE @cdmDatabaseSchema.MEASUREMENT (
unit_source_value varchar(50) NULL,
unit_source_concept_id integer NULL,
value_source_value varchar(50) NULL,
measurement_event_id NUMBER(19) NULL,
measurement_event_id integer NULL,
meas_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
@ -204,7 +204,7 @@ CREATE TABLE @cdmDatabaseSchema.OBSERVATION (
unit_source_value varchar(50) NULL,
qualifier_source_value varchar(50) NULL,
value_source_value varchar(50) NULL,
observation_event_id NUMBER(19) NULL,
observation_event_id integer NULL,
obs_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
@ -233,7 +233,7 @@ CREATE TABLE @cdmDatabaseSchema.NOTE (
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
note_source_value varchar(50) NULL,
note_event_id NUMBER(19) NULL,
note_event_id integer NULL,
note_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON RANDOM
@ -369,8 +369,8 @@ CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date TIMESTAMP NOT NULL,
drug_era_end_date TIMESTAMP NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL );
@ -381,28 +381,28 @@ CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value float NOT NULL,
dose_era_start_date TIMESTAMP NOT NULL,
dose_era_end_date TIMESTAMP NOT NULL );
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date TIMESTAMP NOT NULL,
condition_era_end_date TIMESTAMP NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id NUMBER(19) NOT NULL,
person_id NUMBER(19) NOT NULL,
episode_id integer NOT NULL,
person_id integer NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime TIMESTAMP NULL,
episode_end_date date NULL,
episode_end_datetime TIMESTAMP NULL,
episode_parent_id NUMBER(19) NULL,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -411,8 +411,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id NUMBER(19) NOT NULL,
event_id NUMBER(19) NOT NULL,
episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM

2
inst/ddl/5.4/pdw/OMOPCDM_pdw_5.4_constraints.sql
View File

@ -350,8 +350,6 @@ ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_nu
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_denominator_unit_concept_id FOREIGN KEY (denominator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_cohort_definition_id FOREIGN KEY (cohort_definition_id) REFERENCES @cdmDatabaseSchema.COHORT (COHORT_DEFINITION_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_definition_type_concept_id FOREIGN KEY (definition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_subject_concept_id FOREIGN KEY (subject_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

28
inst/ddl/5.4/pdw/OMOPCDM_pdw_5.4_ddl.sql
View File

@ -179,7 +179,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.MEASUREMENT (measu
unit_source_value varchar(50) NULL,
unit_source_concept_id integer NULL,
value_source_value varchar(50) NULL,
measurement_event_id bigint NULL,
measurement_event_id integer NULL,
meas_event_field_concept_id integer NULL )
WITH (DISTRIBUTION = HASH(person_id));
@ -203,7 +203,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.OBSERVATION (obser
unit_source_value varchar(50) NULL,
qualifier_source_value varchar(50) NULL,
value_source_value varchar(50) NULL,
observation_event_id bigint NULL,
observation_event_id integer NULL,
obs_event_field_concept_id integer NULL )
WITH (DISTRIBUTION = HASH(person_id));
@ -232,7 +232,7 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.NOTE (note_id inte
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
note_source_value varchar(50) NULL,
note_event_id bigint NULL,
note_event_id integer NULL,
note_event_field_concept_id integer NULL )
WITH (DISTRIBUTION = HASH(person_id));
@ -368,8 +368,8 @@ WITH (DISTRIBUTION = REPLICATE);
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date datetime NOT NULL,
drug_era_end_date datetime NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL )
WITH (DISTRIBUTION = HASH(person_id));
@ -380,28 +380,28 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (dose_era
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value float NOT NULL,
dose_era_start_date datetime NOT NULL,
dose_era_end_date datetime NOT NULL )
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL )
WITH (DISTRIBUTION = HASH(person_id));
--HINT DISTRIBUTE ON KEY (person_id)
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date datetime NOT NULL,
condition_era_end_date datetime NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL )
WITH (DISTRIBUTION = HASH(person_id));
--HINT DISTRIBUTE ON KEY (person_id)
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_id bigint NOT NULL,
person_id bigint NOT NULL,
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_id integer NOT NULL,
person_id integer NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime datetime NULL,
episode_end_date date NULL,
episode_end_datetime datetime NULL,
episode_parent_id bigint NULL,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -410,8 +410,8 @@ IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_i
WITH (DISTRIBUTION = HASH(person_id));
--HINT DISTRIBUTE ON RANDOM
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (episode_id bigint NOT NULL,
event_id bigint NOT NULL,
IF XACT_STATE() = 1 COMMIT; CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL )
WITH (DISTRIBUTION = REPLICATE);

2
inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_constraints.sql
View File

@ -350,8 +350,6 @@ ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_nu
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_denominator_unit_concept_id FOREIGN KEY (denominator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_cohort_definition_id FOREIGN KEY (cohort_definition_id) REFERENCES @cdmDatabaseSchema.COHORT (COHORT_DEFINITION_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_definition_type_concept_id FOREIGN KEY (definition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_subject_concept_id FOREIGN KEY (subject_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

28
inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_ddl.sql
View File

@ -180,7 +180,7 @@ CREATE TABLE @cdmDatabaseSchema.MEASUREMENT (
unit_source_value varchar(50) NULL,
unit_source_concept_id integer NULL,
value_source_value varchar(50) NULL,
measurement_event_id bigint NULL,
measurement_event_id integer NULL,
meas_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
@ -204,7 +204,7 @@ CREATE TABLE @cdmDatabaseSchema.OBSERVATION (
unit_source_value varchar(50) NULL,
qualifier_source_value varchar(50) NULL,
value_source_value varchar(50) NULL,
observation_event_id bigint NULL,
observation_event_id integer NULL,
obs_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
@ -233,7 +233,7 @@ CREATE TABLE @cdmDatabaseSchema.NOTE (
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
note_source_value varchar(50) NULL,
note_event_id bigint NULL,
note_event_id integer NULL,
note_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON RANDOM
@ -369,8 +369,8 @@ CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date TIMESTAMP NOT NULL,
drug_era_end_date TIMESTAMP NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL );
@ -381,28 +381,28 @@ CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value NUMERIC NOT NULL,
dose_era_start_date TIMESTAMP NOT NULL,
dose_era_end_date TIMESTAMP NOT NULL );
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date TIMESTAMP NOT NULL,
condition_era_end_date TIMESTAMP NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_id integer NOT NULL,
person_id integer NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime TIMESTAMP NULL,
episode_end_date date NULL,
episode_end_datetime TIMESTAMP NULL,
episode_parent_id bigint NULL,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -411,8 +411,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM

2
inst/ddl/5.4/redshift/OMOPCDM_redshift_5.4_constraints.sql
View File

@ -350,8 +350,6 @@ ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_nu
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_denominator_unit_concept_id FOREIGN KEY (denominator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_cohort_definition_id FOREIGN KEY (cohort_definition_id) REFERENCES @cdmDatabaseSchema.COHORT (COHORT_DEFINITION_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_definition_type_concept_id FOREIGN KEY (definition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_subject_concept_id FOREIGN KEY (subject_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

28
inst/ddl/5.4/redshift/OMOPCDM_redshift_5.4_ddl.sql
View File

@ -179,7 +179,7 @@ CREATE TABLE @cdmDatabaseSchema.MEASUREMENT (measurement_id integer NOT NULL,
unit_source_value varchar(50) NULL,
unit_source_concept_id integer NULL,
value_source_value varchar(50) NULL,
measurement_event_id bigint NULL,
measurement_event_id integer NULL,
meas_event_field_concept_id integer NULL )
DISTKEY(person_id);
@ -203,7 +203,7 @@ CREATE TABLE @cdmDatabaseSchema.OBSERVATION (observation_id integer NOT NULL,
unit_source_value varchar(50) NULL,
qualifier_source_value varchar(50) NULL,
value_source_value varchar(50) NULL,
observation_event_id bigint NULL,
observation_event_id integer NULL,
obs_event_field_concept_id integer NULL )
DISTKEY(person_id);
@ -232,7 +232,7 @@ CREATE TABLE @cdmDatabaseSchema.NOTE (note_id integer NOT NULL,
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
note_source_value varchar(50) NULL,
note_event_id bigint NULL,
note_event_id integer NULL,
note_event_field_concept_id integer NULL )
DISTKEY(person_id);
@ -368,8 +368,8 @@ DISTSTYLE ALL;
CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date TIMESTAMP NOT NULL,
drug_era_end_date TIMESTAMP NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL )
DISTKEY(person_id);
@ -380,28 +380,28 @@ CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (dose_era_id integer NOT NULL,
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value float NOT NULL,
dose_era_start_date TIMESTAMP NOT NULL,
dose_era_end_date TIMESTAMP NOT NULL )
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL )
DISTKEY(person_id);
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date TIMESTAMP NOT NULL,
condition_era_end_date TIMESTAMP NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL )
DISTKEY(person_id);
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_id bigint NOT NULL,
person_id bigint NOT NULL,
CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_id integer NOT NULL,
person_id integer NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime TIMESTAMP NULL,
episode_end_date date NULL,
episode_end_datetime TIMESTAMP NULL,
episode_parent_id bigint NULL,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -410,8 +410,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (episode_id bigint NOT NULL,
DISTKEY(person_id);
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (episode_id bigint NOT NULL,
event_id bigint NOT NULL,
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL )
DISTSTYLE ALL;

177
inst/ddl/5.4/spark/OMOPCDM_spark_5.4_constraints.sql Normal file
View File

@ -0,0 +1,177 @@
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_gender_concept_id FOREIGN KEY (gender_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_race_concept_id FOREIGN KEY (race_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_ethnicity_concept_id FOREIGN KEY (ethnicity_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_location_id FOREIGN KEY (location_id) REFERENCES @cdmDatabaseSchema.LOCATION (LOCATION_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_gender_source_concept_id FOREIGN KEY (gender_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_race_source_concept_id FOREIGN KEY (race_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT fpk_PERSON_ethnicity_source_concept_id FOREIGN KEY (ethnicity_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD ADD CONSTRAINT fpk_OBSERVATION_PERIOD_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD ADD CONSTRAINT fpk_OBSERVATION_PERIOD_period_type_concept_id FOREIGN KEY (period_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_visit_concept_id FOREIGN KEY (visit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_visit_type_concept_id FOREIGN KEY (visit_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_visit_source_concept_id FOREIGN KEY (visit_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_admitted_from_concept_id FOREIGN KEY (admitted_from_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_discharged_to_concept_id FOREIGN KEY (discharged_to_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT fpk_VISIT_OCCURRENCE_preceding_visit_occurrence_id FOREIGN KEY (preceding_visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_detail_concept_id FOREIGN KEY (visit_detail_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_detail_type_concept_id FOREIGN KEY (visit_detail_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_detail_source_concept_id FOREIGN KEY (visit_detail_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_admitted_from_concept_id FOREIGN KEY (admitted_from_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_discharged_to_concept_id FOREIGN KEY (discharged_to_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_preceding_visit_detail_id FOREIGN KEY (preceding_visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_parent_visit_detail_id FOREIGN KEY (parent_visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT fpk_VISIT_DETAIL_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_concept_id FOREIGN KEY (condition_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_type_concept_id FOREIGN KEY (condition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_status_concept_id FOREIGN KEY (condition_status_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT fpk_CONDITION_OCCURRENCE_condition_source_concept_id FOREIGN KEY (condition_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_drug_type_concept_id FOREIGN KEY (drug_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_route_concept_id FOREIGN KEY (route_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT fpk_DRUG_EXPOSURE_drug_source_concept_id FOREIGN KEY (drug_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_procedure_concept_id FOREIGN KEY (procedure_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_procedure_type_concept_id FOREIGN KEY (procedure_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_modifier_concept_id FOREIGN KEY (modifier_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT fpk_PROCEDURE_OCCURRENCE_procedure_source_concept_id FOREIGN KEY (procedure_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_device_concept_id FOREIGN KEY (device_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_device_type_concept_id FOREIGN KEY (device_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_device_source_concept_id FOREIGN KEY (device_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT fpk_DEVICE_EXPOSURE_unit_source_concept_id FOREIGN KEY (unit_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_measurement_concept_id FOREIGN KEY (measurement_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_measurement_type_concept_id FOREIGN KEY (measurement_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_operator_concept_id FOREIGN KEY (operator_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_value_as_concept_id FOREIGN KEY (value_as_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_measurement_source_concept_id FOREIGN KEY (measurement_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_unit_source_concept_id FOREIGN KEY (unit_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT fpk_MEASUREMENT_meas_event_field_concept_id FOREIGN KEY (meas_event_field_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_observation_concept_id FOREIGN KEY (observation_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_observation_type_concept_id FOREIGN KEY (observation_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_value_as_concept_id FOREIGN KEY (value_as_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_qualifier_concept_id FOREIGN KEY (qualifier_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_observation_source_concept_id FOREIGN KEY (observation_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT fpk_OBSERVATION_obs_event_field_concept_id FOREIGN KEY (obs_event_field_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_death_type_concept_id FOREIGN KEY (death_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_cause_concept_id FOREIGN KEY (cause_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DEATH ADD CONSTRAINT fpk_DEATH_cause_source_concept_id FOREIGN KEY (cause_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_note_type_concept_id FOREIGN KEY (note_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_note_class_concept_id FOREIGN KEY (note_class_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_encoding_concept_id FOREIGN KEY (encoding_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_language_concept_id FOREIGN KEY (language_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_provider_id FOREIGN KEY (provider_id) REFERENCES @cdmDatabaseSchema.PROVIDER (PROVIDER_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_visit_occurrence_id FOREIGN KEY (visit_occurrence_id) REFERENCES @cdmDatabaseSchema.VISIT_OCCURRENCE (VISIT_OCCURRENCE_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_visit_detail_id FOREIGN KEY (visit_detail_id) REFERENCES @cdmDatabaseSchema.VISIT_DETAIL (VISIT_DETAIL_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT fpk_NOTE_note_event_field_concept_id FOREIGN KEY (note_event_field_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT fpk_NOTE_NLP_section_concept_id FOREIGN KEY (section_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT fpk_NOTE_NLP_note_nlp_concept_id FOREIGN KEY (note_nlp_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT fpk_NOTE_NLP_note_nlp_source_concept_id FOREIGN KEY (note_nlp_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_specimen_concept_id FOREIGN KEY (specimen_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_specimen_type_concept_id FOREIGN KEY (specimen_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_anatomic_site_concept_id FOREIGN KEY (anatomic_site_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT fpk_SPECIMEN_disease_status_concept_id FOREIGN KEY (disease_status_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP ADD CONSTRAINT fpk_FACT_RELATIONSHIP_domain_concept_id_1 FOREIGN KEY (domain_concept_id_1) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP ADD CONSTRAINT fpk_FACT_RELATIONSHIP_domain_concept_id_2 FOREIGN KEY (domain_concept_id_2) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP ADD CONSTRAINT fpk_FACT_RELATIONSHIP_relationship_concept_id FOREIGN KEY (relationship_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.LOCATION ADD CONSTRAINT fpk_LOCATION_country_concept_id FOREIGN KEY (country_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CARE_SITE ADD CONSTRAINT fpk_CARE_SITE_place_of_service_concept_id FOREIGN KEY (place_of_service_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CARE_SITE ADD CONSTRAINT fpk_CARE_SITE_location_id FOREIGN KEY (location_id) REFERENCES @cdmDatabaseSchema.LOCATION (LOCATION_ID);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_specialty_concept_id FOREIGN KEY (specialty_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_care_site_id FOREIGN KEY (care_site_id) REFERENCES @cdmDatabaseSchema.CARE_SITE (CARE_SITE_ID);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_gender_concept_id FOREIGN KEY (gender_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_specialty_source_concept_id FOREIGN KEY (specialty_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT fpk_PROVIDER_gender_source_concept_id FOREIGN KEY (gender_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_payer_plan_period_id FOREIGN KEY (payer_plan_period_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_payer_concept_id FOREIGN KEY (payer_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_payer_source_concept_id FOREIGN KEY (payer_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_plan_concept_id FOREIGN KEY (plan_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_plan_source_concept_id FOREIGN KEY (plan_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_sponsor_concept_id FOREIGN KEY (sponsor_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_sponsor_source_concept_id FOREIGN KEY (sponsor_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_stop_reason_concept_id FOREIGN KEY (stop_reason_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT fpk_PAYER_PLAN_PERIOD_stop_reason_source_concept_id FOREIGN KEY (stop_reason_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_cost_domain_id FOREIGN KEY (cost_domain_id) REFERENCES @cdmDatabaseSchema.DOMAIN (DOMAIN_ID);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_cost_type_concept_id FOREIGN KEY (cost_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_currency_concept_id FOREIGN KEY (currency_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_revenue_code_concept_id FOREIGN KEY (revenue_code_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT fpk_COST_drg_concept_id FOREIGN KEY (drg_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_ERA ADD CONSTRAINT fpk_DRUG_ERA_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_ERA ADD CONSTRAINT fpk_DRUG_ERA_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT fpk_DOSE_ERA_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT fpk_DOSE_ERA_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT fpk_DOSE_ERA_unit_concept_id FOREIGN KEY (unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT fpk_CONDITION_ERA_condition_concept_id FOREIGN KEY (condition_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_person_id FOREIGN KEY (person_id) REFERENCES @cdmDatabaseSchema.PERSON (PERSON_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_concept_id FOREIGN KEY (episode_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_object_concept_id FOREIGN KEY (episode_object_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_type_concept_id FOREIGN KEY (episode_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT fpk_EPISODE_episode_source_concept_id FOREIGN KEY (episode_source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE_EVENT ADD CONSTRAINT fpk_EPISODE_EVENT_episode_id FOREIGN KEY (episode_id) REFERENCES @cdmDatabaseSchema.EPISODE (EPISODE_ID);
ALTER TABLE @cdmDatabaseSchema.EPISODE_EVENT ADD CONSTRAINT fpk_EPISODE_EVENT_episode_event_field_concept_id FOREIGN KEY (episode_event_field_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT fpk_METADATA_metadata_concept_id FOREIGN KEY (metadata_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT fpk_METADATA_metadata_type_concept_id FOREIGN KEY (metadata_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT fpk_METADATA_value_as_concept_id FOREIGN KEY (value_as_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CDM_SOURCE ADD CONSTRAINT fpk_CDM_SOURCE_cdm_version_concept_id FOREIGN KEY (cdm_version_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT fpk_CONCEPT_domain_id FOREIGN KEY (domain_id) REFERENCES @cdmDatabaseSchema.DOMAIN (DOMAIN_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT fpk_CONCEPT_vocabulary_id FOREIGN KEY (vocabulary_id) REFERENCES @cdmDatabaseSchema.VOCABULARY (VOCABULARY_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT fpk_CONCEPT_concept_class_id FOREIGN KEY (concept_class_id) REFERENCES @cdmDatabaseSchema.CONCEPT_CLASS (CONCEPT_CLASS_ID);
ALTER TABLE @cdmDatabaseSchema.VOCABULARY ADD CONSTRAINT fpk_VOCABULARY_vocabulary_concept_id FOREIGN KEY (vocabulary_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DOMAIN ADD CONSTRAINT fpk_DOMAIN_domain_concept_id FOREIGN KEY (domain_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_CLASS ADD CONSTRAINT fpk_CONCEPT_CLASS_concept_class_concept_id FOREIGN KEY (concept_class_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP ADD CONSTRAINT fpk_CONCEPT_RELATIONSHIP_concept_id_1 FOREIGN KEY (concept_id_1) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP ADD CONSTRAINT fpk_CONCEPT_RELATIONSHIP_concept_id_2 FOREIGN KEY (concept_id_2) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP ADD CONSTRAINT fpk_CONCEPT_RELATIONSHIP_relationship_id FOREIGN KEY (relationship_id) REFERENCES @cdmDatabaseSchema.RELATIONSHIP (RELATIONSHIP_ID);
ALTER TABLE @cdmDatabaseSchema.RELATIONSHIP ADD CONSTRAINT fpk_RELATIONSHIP_relationship_concept_id FOREIGN KEY (relationship_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM ADD CONSTRAINT fpk_CONCEPT_SYNONYM_concept_id FOREIGN KEY (concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM ADD CONSTRAINT fpk_CONCEPT_SYNONYM_language_concept_id FOREIGN KEY (language_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR ADD CONSTRAINT fpk_CONCEPT_ANCESTOR_ancestor_concept_id FOREIGN KEY (ancestor_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR ADD CONSTRAINT fpk_CONCEPT_ANCESTOR_descendant_concept_id FOREIGN KEY (descendant_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP ADD CONSTRAINT fpk_SOURCE_TO_CONCEPT_MAP_source_concept_id FOREIGN KEY (source_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP ADD CONSTRAINT fpk_SOURCE_TO_CONCEPT_MAP_target_concept_id FOREIGN KEY (target_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP ADD CONSTRAINT fpk_SOURCE_TO_CONCEPT_MAP_target_vocabulary_id FOREIGN KEY (target_vocabulary_id) REFERENCES @cdmDatabaseSchema.VOCABULARY (VOCABULARY_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_drug_concept_id FOREIGN KEY (drug_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_ingredient_concept_id FOREIGN KEY (ingredient_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_amount_unit_concept_id FOREIGN KEY (amount_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_numerator_unit_concept_id FOREIGN KEY (numerator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_denominator_unit_concept_id FOREIGN KEY (denominator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_definition_type_concept_id FOREIGN KEY (definition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_subject_concept_id FOREIGN KEY (subject_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

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--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.PERSON
USING DELTA
AS
SELECT CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS gender_concept_id,
CAST(NULL AS integer) AS year_of_birth,
CAST(NULL AS integer) AS month_of_birth,
CAST(NULL AS integer) AS day_of_birth,
CAST(NULL AS TIMESTAMP) AS birth_datetime,
CAST(NULL AS integer) AS race_concept_id,
CAST(NULL AS integer) AS ethnicity_concept_id,
CAST(NULL AS integer) AS location_id,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS care_site_id,
CAST(NULL AS STRING) AS person_source_value,
CAST(NULL AS STRING) AS gender_source_value,
CAST(NULL AS integer) AS gender_source_concept_id,
CAST(NULL AS STRING) AS race_source_value,
CAST(NULL AS integer) AS race_source_concept_id,
CAST(NULL AS STRING) AS ethnicity_source_value,
CAST(NULL AS integer) AS ethnicity_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD
USING DELTA
AS
SELECT CAST(NULL AS integer) AS observation_period_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS date) AS observation_period_start_date,
CAST(NULL AS date) AS observation_period_end_date,
CAST(NULL AS integer) AS period_type_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS visit_concept_id,
CAST(NULL AS date) AS visit_start_date,
CAST(NULL AS TIMESTAMP) AS visit_start_datetime,
CAST(NULL AS date) AS visit_end_date,
CAST(NULL AS TIMESTAMP) AS visit_end_datetime,
CAST(NULL AS integer) AS visit_type_concept_id,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS care_site_id,
CAST(NULL AS STRING) AS visit_source_value,
CAST(NULL AS integer) AS visit_source_concept_id,
CAST(NULL AS integer) AS admitted_from_concept_id,
CAST(NULL AS STRING) AS admitted_from_source_value,
CAST(NULL AS integer) AS discharged_to_concept_id,
CAST(NULL AS STRING) AS discharged_to_source_value,
CAST(NULL AS integer) AS preceding_visit_occurrence_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.VISIT_DETAIL
USING DELTA
AS
SELECT CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS visit_detail_concept_id,
CAST(NULL AS date) AS visit_detail_start_date,
CAST(NULL AS TIMESTAMP) AS visit_detail_start_datetime,
CAST(NULL AS date) AS visit_detail_end_date,
CAST(NULL AS TIMESTAMP) AS visit_detail_end_datetime,
CAST(NULL AS integer) AS visit_detail_type_concept_id,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS care_site_id,
CAST(NULL AS STRING) AS visit_detail_source_value,
CAST(NULL AS integer) AS visit_detail_source_concept_id,
CAST(NULL AS integer) AS admitted_from_concept_id,
CAST(NULL AS STRING) AS admitted_from_source_value,
CAST(NULL AS STRING) AS discharged_to_source_value,
CAST(NULL AS integer) AS discharged_to_concept_id,
CAST(NULL AS integer) AS preceding_visit_detail_id,
CAST(NULL AS integer) AS parent_visit_detail_id,
CAST(NULL AS integer) AS visit_occurrence_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS condition_occurrence_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS condition_concept_id,
CAST(NULL AS date) AS condition_start_date,
CAST(NULL AS TIMESTAMP) AS condition_start_datetime,
CAST(NULL AS date) AS condition_end_date,
CAST(NULL AS TIMESTAMP) AS condition_end_datetime,
CAST(NULL AS integer) AS condition_type_concept_id,
CAST(NULL AS integer) AS condition_status_concept_id,
CAST(NULL AS STRING) AS stop_reason,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS condition_source_value,
CAST(NULL AS integer) AS condition_source_concept_id,
CAST(NULL AS STRING) AS condition_status_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DRUG_EXPOSURE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS drug_exposure_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS drug_concept_id,
CAST(NULL AS date) AS drug_exposure_start_date,
CAST(NULL AS TIMESTAMP) AS drug_exposure_start_datetime,
CAST(NULL AS date) AS drug_exposure_end_date,
CAST(NULL AS TIMESTAMP) AS drug_exposure_end_datetime,
CAST(NULL AS date) AS verbatim_end_date,
CAST(NULL AS integer) AS drug_type_concept_id,
CAST(NULL AS STRING) AS stop_reason,
CAST(NULL AS integer) AS refills,
CAST(NULL AS float) AS quantity,
CAST(NULL AS integer) AS days_supply,
CAST(NULL AS STRING) AS sig,
CAST(NULL AS integer) AS route_concept_id,
CAST(NULL AS STRING) AS lot_number,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS drug_source_value,
CAST(NULL AS integer) AS drug_source_concept_id,
CAST(NULL AS STRING) AS route_source_value,
CAST(NULL AS STRING) AS dose_unit_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS procedure_occurrence_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS procedure_concept_id,
CAST(NULL AS date) AS procedure_date,
CAST(NULL AS TIMESTAMP) AS procedure_datetime,
CAST(NULL AS date) AS procedure_end_date,
CAST(NULL AS TIMESTAMP) AS procedure_end_datetime,
CAST(NULL AS integer) AS procedure_type_concept_id,
CAST(NULL AS integer) AS modifier_concept_id,
CAST(NULL AS integer) AS quantity,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS procedure_source_value,
CAST(NULL AS integer) AS procedure_source_concept_id,
CAST(NULL AS STRING) AS modifier_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS device_exposure_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS device_concept_id,
CAST(NULL AS date) AS device_exposure_start_date,
CAST(NULL AS TIMESTAMP) AS device_exposure_start_datetime,
CAST(NULL AS date) AS device_exposure_end_date,
CAST(NULL AS TIMESTAMP) AS device_exposure_end_datetime,
CAST(NULL AS integer) AS device_type_concept_id,
CAST(NULL AS STRING) AS unique_device_id,
CAST(NULL AS STRING) AS production_id,
CAST(NULL AS integer) AS quantity,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS device_source_value,
CAST(NULL AS integer) AS device_source_concept_id,
CAST(NULL AS integer) AS unit_concept_id,
CAST(NULL AS STRING) AS unit_source_value,
CAST(NULL AS integer) AS unit_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.MEASUREMENT
USING DELTA
AS
SELECT CAST(NULL AS integer) AS measurement_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS measurement_concept_id,
CAST(NULL AS date) AS measurement_date,
CAST(NULL AS TIMESTAMP) AS measurement_datetime,
CAST(NULL AS STRING) AS measurement_time,
CAST(NULL AS integer) AS measurement_type_concept_id,
CAST(NULL AS integer) AS operator_concept_id,
CAST(NULL AS float) AS value_as_number,
CAST(NULL AS integer) AS value_as_concept_id,
CAST(NULL AS integer) AS unit_concept_id,
CAST(NULL AS float) AS range_low,
CAST(NULL AS float) AS range_high,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS measurement_source_value,
CAST(NULL AS integer) AS measurement_source_concept_id,
CAST(NULL AS STRING) AS unit_source_value,
CAST(NULL AS integer) AS unit_source_concept_id,
CAST(NULL AS STRING) AS value_source_value,
CAST(NULL AS integer) AS measurement_event_id,
CAST(NULL AS integer) AS meas_event_field_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.OBSERVATION
USING DELTA
AS
SELECT CAST(NULL AS integer) AS observation_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS observation_concept_id,
CAST(NULL AS date) AS observation_date,
CAST(NULL AS TIMESTAMP) AS observation_datetime,
CAST(NULL AS integer) AS observation_type_concept_id,
CAST(NULL AS float) AS value_as_number,
CAST(NULL AS STRING) AS value_as_string,
CAST(NULL AS integer) AS value_as_concept_id,
CAST(NULL AS integer) AS qualifier_concept_id,
CAST(NULL AS integer) AS unit_concept_id,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS observation_source_value,
CAST(NULL AS integer) AS observation_source_concept_id,
CAST(NULL AS STRING) AS unit_source_value,
CAST(NULL AS STRING) AS qualifier_source_value,
CAST(NULL AS STRING) AS value_source_value,
CAST(NULL AS integer) AS observation_event_id,
CAST(NULL AS integer) AS obs_event_field_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DEATH
USING DELTA
AS
SELECT CAST(NULL AS integer) AS person_id,
CAST(NULL AS date) AS death_date,
CAST(NULL AS TIMESTAMP) AS death_datetime,
CAST(NULL AS integer) AS death_type_concept_id,
CAST(NULL AS integer) AS cause_concept_id,
CAST(NULL AS STRING) AS cause_source_value,
CAST(NULL AS integer) AS cause_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.NOTE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS note_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS date) AS note_date,
CAST(NULL AS TIMESTAMP) AS note_datetime,
CAST(NULL AS integer) AS note_type_concept_id,
CAST(NULL AS integer) AS note_class_concept_id,
CAST(NULL AS STRING) AS note_title,
CAST(NULL AS STRING) AS note_text,
CAST(NULL AS integer) AS encoding_concept_id,
CAST(NULL AS integer) AS language_concept_id,
CAST(NULL AS integer) AS provider_id,
CAST(NULL AS integer) AS visit_occurrence_id,
CAST(NULL AS integer) AS visit_detail_id,
CAST(NULL AS STRING) AS note_source_value,
CAST(NULL AS integer) AS note_event_id,
CAST(NULL AS integer) AS note_event_field_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.NOTE_NLP
USING DELTA
AS
SELECT CAST(NULL AS integer) AS note_nlp_id,
CAST(NULL AS integer) AS note_id,
CAST(NULL AS integer) AS section_concept_id,
CAST(NULL AS STRING) AS snippet,
CAST(NULL AS STRING) AS offset,
CAST(NULL AS STRING) AS lexical_variant,
CAST(NULL AS integer) AS note_nlp_concept_id,
CAST(NULL AS integer) AS note_nlp_source_concept_id,
CAST(NULL AS STRING) AS nlp_system,
CAST(NULL AS date) AS nlp_date,
CAST(NULL AS TIMESTAMP) AS nlp_datetime,
CAST(NULL AS STRING) AS term_exists,
CAST(NULL AS STRING) AS term_temporal,
CAST(NULL AS STRING) AS term_modifiers WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.SPECIMEN
USING DELTA
AS
SELECT CAST(NULL AS integer) AS specimen_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS specimen_concept_id,
CAST(NULL AS integer) AS specimen_type_concept_id,
CAST(NULL AS date) AS specimen_date,
CAST(NULL AS TIMESTAMP) AS specimen_datetime,
CAST(NULL AS float) AS quantity,
CAST(NULL AS integer) AS unit_concept_id,
CAST(NULL AS integer) AS anatomic_site_concept_id,
CAST(NULL AS integer) AS disease_status_concept_id,
CAST(NULL AS STRING) AS specimen_source_id,
CAST(NULL AS STRING) AS specimen_source_value,
CAST(NULL AS STRING) AS unit_source_value,
CAST(NULL AS STRING) AS anatomic_site_source_value,
CAST(NULL AS STRING) AS disease_status_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.FACT_RELATIONSHIP
USING DELTA
AS
SELECT CAST(NULL AS integer) AS domain_concept_id_1,
CAST(NULL AS integer) AS fact_id_1,
CAST(NULL AS integer) AS domain_concept_id_2,
CAST(NULL AS integer) AS fact_id_2,
CAST(NULL AS integer) AS relationship_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.LOCATION
USING DELTA
AS
SELECT CAST(NULL AS integer) AS location_id,
CAST(NULL AS STRING) AS address_1,
CAST(NULL AS STRING) AS address_2,
CAST(NULL AS STRING) AS city,
CAST(NULL AS STRING) AS state,
CAST(NULL AS STRING) AS zip,
CAST(NULL AS STRING) AS county,
CAST(NULL AS STRING) AS location_source_value,
CAST(NULL AS integer) AS country_concept_id,
CAST(NULL AS STRING) AS country_source_value,
CAST(NULL AS float) AS latitude,
CAST(NULL AS float) AS longitude WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CARE_SITE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS care_site_id,
CAST(NULL AS STRING) AS care_site_name,
CAST(NULL AS integer) AS place_of_service_concept_id,
CAST(NULL AS integer) AS location_id,
CAST(NULL AS STRING) AS care_site_source_value,
CAST(NULL AS STRING) AS place_of_service_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.PROVIDER
USING DELTA
AS
SELECT CAST(NULL AS integer) AS provider_id,
CAST(NULL AS STRING) AS provider_name,
CAST(NULL AS STRING) AS npi,
CAST(NULL AS STRING) AS dea,
CAST(NULL AS integer) AS specialty_concept_id,
CAST(NULL AS integer) AS care_site_id,
CAST(NULL AS integer) AS year_of_birth,
CAST(NULL AS integer) AS gender_concept_id,
CAST(NULL AS STRING) AS provider_source_value,
CAST(NULL AS STRING) AS specialty_source_value,
CAST(NULL AS integer) AS specialty_source_concept_id,
CAST(NULL AS STRING) AS gender_source_value,
CAST(NULL AS integer) AS gender_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD
USING DELTA
AS
SELECT CAST(NULL AS integer) AS payer_plan_period_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS date) AS payer_plan_period_start_date,
CAST(NULL AS date) AS payer_plan_period_end_date,
CAST(NULL AS integer) AS payer_concept_id,
CAST(NULL AS STRING) AS payer_source_value,
CAST(NULL AS integer) AS payer_source_concept_id,
CAST(NULL AS integer) AS plan_concept_id,
CAST(NULL AS STRING) AS plan_source_value,
CAST(NULL AS integer) AS plan_source_concept_id,
CAST(NULL AS integer) AS sponsor_concept_id,
CAST(NULL AS STRING) AS sponsor_source_value,
CAST(NULL AS integer) AS sponsor_source_concept_id,
CAST(NULL AS STRING) AS family_source_value,
CAST(NULL AS integer) AS stop_reason_concept_id,
CAST(NULL AS STRING) AS stop_reason_source_value,
CAST(NULL AS integer) AS stop_reason_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.COST
USING DELTA
AS
SELECT CAST(NULL AS integer) AS cost_id,
CAST(NULL AS integer) AS cost_event_id,
CAST(NULL AS STRING) AS cost_domain_id,
CAST(NULL AS integer) AS cost_type_concept_id,
CAST(NULL AS integer) AS currency_concept_id,
CAST(NULL AS float) AS total_charge,
CAST(NULL AS float) AS total_cost,
CAST(NULL AS float) AS total_paid,
CAST(NULL AS float) AS paid_by_payer,
CAST(NULL AS float) AS paid_by_patient,
CAST(NULL AS float) AS paid_patient_copay,
CAST(NULL AS float) AS paid_patient_coinsurance,
CAST(NULL AS float) AS paid_patient_deductible,
CAST(NULL AS float) AS paid_by_primary,
CAST(NULL AS float) AS paid_ingredient_cost,
CAST(NULL AS float) AS paid_dispensing_fee,
CAST(NULL AS integer) AS payer_plan_period_id,
CAST(NULL AS float) AS amount_allowed,
CAST(NULL AS integer) AS revenue_code_concept_id,
CAST(NULL AS STRING) AS revenue_code_source_value,
CAST(NULL AS integer) AS drg_concept_id,
CAST(NULL AS STRING) AS drg_source_value WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DRUG_ERA
USING DELTA
AS
SELECT CAST(NULL AS integer) AS drug_era_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS drug_concept_id,
CAST(NULL AS date) AS drug_era_start_date,
CAST(NULL AS date) AS drug_era_end_date,
CAST(NULL AS integer) AS drug_exposure_count,
CAST(NULL AS integer) AS gap_days WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.DOSE_ERA
USING DELTA
AS
SELECT CAST(NULL AS integer) AS dose_era_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS drug_concept_id,
CAST(NULL AS integer) AS unit_concept_id,
CAST(NULL AS float) AS dose_value,
CAST(NULL AS date) AS dose_era_start_date,
CAST(NULL AS date) AS dose_era_end_date WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA
USING DELTA
AS
SELECT CAST(NULL AS integer) AS condition_era_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS condition_concept_id,
CAST(NULL AS date) AS condition_era_start_date,
CAST(NULL AS date) AS condition_era_end_date,
CAST(NULL AS integer) AS condition_occurrence_count WHERE 1 = 0;
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE
USING DELTA
AS
SELECT CAST(NULL AS integer) AS episode_id,
CAST(NULL AS integer) AS person_id,
CAST(NULL AS integer) AS episode_concept_id,
CAST(NULL AS date) AS episode_start_date,
CAST(NULL AS TIMESTAMP) AS episode_start_datetime,
CAST(NULL AS date) AS episode_end_date,
CAST(NULL AS TIMESTAMP) AS episode_end_datetime,
CAST(NULL AS integer) AS episode_parent_id,
CAST(NULL AS integer) AS episode_number,
CAST(NULL AS integer) AS episode_object_concept_id,
CAST(NULL AS integer) AS episode_type_concept_id,
CAST(NULL AS STRING) AS episode_source_value,
CAST(NULL AS integer) AS episode_source_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT
USING DELTA
AS
SELECT CAST(NULL AS integer) AS episode_id,
CAST(NULL AS integer) AS event_id,
CAST(NULL AS integer) AS episode_event_field_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.METADATA
USING DELTA
AS
SELECT CAST(NULL AS integer) AS metadata_id,
CAST(NULL AS integer) AS metadata_concept_id,
CAST(NULL AS integer) AS metadata_type_concept_id,
CAST(NULL AS STRING) AS name,
CAST(NULL AS STRING) AS value_as_string,
CAST(NULL AS integer) AS value_as_concept_id,
CAST(NULL AS float) AS value_as_number,
CAST(NULL AS date) AS metadata_date,
CAST(NULL AS TIMESTAMP) AS metadata_datetime WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CDM_SOURCE
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS cdm_source_name,
CAST(NULL AS STRING) AS cdm_source_abbreviation,
CAST(NULL AS STRING) AS cdm_holder,
CAST(NULL AS STRING) AS source_description,
CAST(NULL AS STRING) AS source_documentation_reference,
CAST(NULL AS STRING) AS cdm_etl_reference,
CAST(NULL AS date) AS source_release_date,
CAST(NULL AS date) AS cdm_release_date,
CAST(NULL AS STRING) AS cdm_version,
CAST(NULL AS integer) AS cdm_version_concept_id,
CAST(NULL AS STRING) AS vocabulary_version WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT
USING DELTA
AS
SELECT CAST(NULL AS integer) AS concept_id,
CAST(NULL AS STRING) AS concept_name,
CAST(NULL AS STRING) AS domain_id,
CAST(NULL AS STRING) AS vocabulary_id,
CAST(NULL AS STRING) AS concept_class_id,
CAST(NULL AS STRING) AS standard_concept,
CAST(NULL AS STRING) AS concept_code,
CAST(NULL AS date) AS valid_start_date,
CAST(NULL AS date) AS valid_end_date,
CAST(NULL AS STRING) AS invalid_reason WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.VOCABULARY
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS vocabulary_id,
CAST(NULL AS STRING) AS vocabulary_name,
CAST(NULL AS STRING) AS vocabulary_reference,
CAST(NULL AS STRING) AS vocabulary_version,
CAST(NULL AS integer) AS vocabulary_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.DOMAIN
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS domain_id,
CAST(NULL AS STRING) AS domain_name,
CAST(NULL AS integer) AS domain_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT_CLASS
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS concept_class_id,
CAST(NULL AS STRING) AS concept_class_name,
CAST(NULL AS integer) AS concept_class_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT_RELATIONSHIP
USING DELTA
AS
SELECT CAST(NULL AS integer) AS concept_id_1,
CAST(NULL AS integer) AS concept_id_2,
CAST(NULL AS STRING) AS relationship_id,
CAST(NULL AS date) AS valid_start_date,
CAST(NULL AS date) AS valid_end_date,
CAST(NULL AS STRING) AS invalid_reason WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.RELATIONSHIP
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS relationship_id,
CAST(NULL AS STRING) AS relationship_name,
CAST(NULL AS STRING) AS is_hierarchical,
CAST(NULL AS STRING) AS defines_ancestry,
CAST(NULL AS STRING) AS reverse_relationship_id,
CAST(NULL AS integer) AS relationship_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT_SYNONYM
USING DELTA
AS
SELECT CAST(NULL AS integer) AS concept_id,
CAST(NULL AS STRING) AS concept_synonym_name,
CAST(NULL AS integer) AS language_concept_id WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.CONCEPT_ANCESTOR
USING DELTA
AS
SELECT CAST(NULL AS integer) AS ancestor_concept_id,
CAST(NULL AS integer) AS descendant_concept_id,
CAST(NULL AS integer) AS min_levels_of_separation,
CAST(NULL AS integer) AS max_levels_of_separation WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.SOURCE_TO_CONCEPT_MAP
USING DELTA
AS
SELECT CAST(NULL AS STRING) AS source_code,
CAST(NULL AS integer) AS source_concept_id,
CAST(NULL AS STRING) AS source_vocabulary_id,
CAST(NULL AS STRING) AS source_code_description,
CAST(NULL AS integer) AS target_concept_id,
CAST(NULL AS STRING) AS target_vocabulary_id,
CAST(NULL AS date) AS valid_start_date,
CAST(NULL AS date) AS valid_end_date,
CAST(NULL AS STRING) AS invalid_reason WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.DRUG_STRENGTH
USING DELTA
AS
SELECT CAST(NULL AS integer) AS drug_concept_id,
CAST(NULL AS integer) AS ingredient_concept_id,
CAST(NULL AS float) AS amount_value,
CAST(NULL AS integer) AS amount_unit_concept_id,
CAST(NULL AS float) AS numerator_value,
CAST(NULL AS integer) AS numerator_unit_concept_id,
CAST(NULL AS float) AS denominator_value,
CAST(NULL AS integer) AS denominator_unit_concept_id,
CAST(NULL AS integer) AS box_size,
CAST(NULL AS date) AS valid_start_date,
CAST(NULL AS date) AS valid_end_date,
CAST(NULL AS STRING) AS invalid_reason WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.COHORT
USING DELTA
AS
SELECT CAST(NULL AS integer) AS cohort_definition_id,
CAST(NULL AS integer) AS subject_id,
CAST(NULL AS date) AS cohort_start_date,
CAST(NULL AS date) AS cohort_end_date WHERE 1 = 0;
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.COHORT_DEFINITION
USING DELTA
AS
SELECT CAST(NULL AS integer) AS cohort_definition_id,
CAST(NULL AS STRING) AS cohort_definition_name,
CAST(NULL AS STRING) AS cohort_definition_description,
CAST(NULL AS integer) AS definition_type_concept_id,
CAST(NULL AS STRING) AS cohort_definition_syntax,
CAST(NULL AS integer) AS subject_concept_id,
CAST(NULL AS date) AS cohort_initiation_date WHERE 1 = 0;

70
inst/ddl/5.4/spark/OMOPCDM_spark_5.4_indices.sql Normal file
View File

@ -0,0 +1,70 @@
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes
-- spark does not support indexes

28
inst/ddl/5.4/spark/OMOPCDM_spark_5.4_primary_keys.sql Normal file
View File

@ -0,0 +1,28 @@
ALTER TABLE @cdmDatabaseSchema.PERSON ADD CONSTRAINT xpk_PERSON (person_id);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION_PERIOD ADD CONSTRAINT xpk_OBSERVATION_PERIOD (observation_period_id);
ALTER TABLE @cdmDatabaseSchema.VISIT_OCCURRENCE ADD CONSTRAINT xpk_VISIT_OCCURRENCE (visit_occurrence_id);
ALTER TABLE @cdmDatabaseSchema.VISIT_DETAIL ADD CONSTRAINT xpk_VISIT_DETAIL (visit_detail_id);
ALTER TABLE @cdmDatabaseSchema.CONDITION_OCCURRENCE ADD CONSTRAINT xpk_CONDITION_OCCURRENCE (condition_occurrence_id);
ALTER TABLE @cdmDatabaseSchema.DRUG_EXPOSURE ADD CONSTRAINT xpk_DRUG_EXPOSURE (drug_exposure_id);
ALTER TABLE @cdmDatabaseSchema.PROCEDURE_OCCURRENCE ADD CONSTRAINT xpk_PROCEDURE_OCCURRENCE (procedure_occurrence_id);
ALTER TABLE @cdmDatabaseSchema.DEVICE_EXPOSURE ADD CONSTRAINT xpk_DEVICE_EXPOSURE (device_exposure_id);
ALTER TABLE @cdmDatabaseSchema.MEASUREMENT ADD CONSTRAINT xpk_MEASUREMENT (measurement_id);
ALTER TABLE @cdmDatabaseSchema.OBSERVATION ADD CONSTRAINT xpk_OBSERVATION (observation_id);
ALTER TABLE @cdmDatabaseSchema.NOTE ADD CONSTRAINT xpk_NOTE (note_id);
ALTER TABLE @cdmDatabaseSchema.NOTE_NLP ADD CONSTRAINT xpk_NOTE_NLP (note_nlp_id);
ALTER TABLE @cdmDatabaseSchema.SPECIMEN ADD CONSTRAINT xpk_SPECIMEN (specimen_id);
ALTER TABLE @cdmDatabaseSchema.LOCATION ADD CONSTRAINT xpk_LOCATION (location_id);
ALTER TABLE @cdmDatabaseSchema.CARE_SITE ADD CONSTRAINT xpk_CARE_SITE (care_site_id);
ALTER TABLE @cdmDatabaseSchema.PROVIDER ADD CONSTRAINT xpk_PROVIDER (provider_id);
ALTER TABLE @cdmDatabaseSchema.PAYER_PLAN_PERIOD ADD CONSTRAINT xpk_PAYER_PLAN_PERIOD (payer_plan_period_id);
ALTER TABLE @cdmDatabaseSchema.COST ADD CONSTRAINT xpk_COST (cost_id);
ALTER TABLE @cdmDatabaseSchema.DRUG_ERA ADD CONSTRAINT xpk_DRUG_ERA (drug_era_id);
ALTER TABLE @cdmDatabaseSchema.DOSE_ERA ADD CONSTRAINT xpk_DOSE_ERA (dose_era_id);
ALTER TABLE @cdmDatabaseSchema.CONDITION_ERA ADD CONSTRAINT xpk_CONDITION_ERA (condition_era_id);
ALTER TABLE @cdmDatabaseSchema.EPISODE ADD CONSTRAINT xpk_EPISODE (episode_id);
ALTER TABLE @cdmDatabaseSchema.METADATA ADD CONSTRAINT xpk_METADATA (metadata_id);
ALTER TABLE @cdmDatabaseSchema.CONCEPT ADD CONSTRAINT xpk_CONCEPT (concept_id);
ALTER TABLE @cdmDatabaseSchema.VOCABULARY ADD CONSTRAINT xpk_VOCABULARY (vocabulary_id);
ALTER TABLE @cdmDatabaseSchema.DOMAIN ADD CONSTRAINT xpk_DOMAIN (domain_id);
ALTER TABLE @cdmDatabaseSchema.CONCEPT_CLASS ADD CONSTRAINT xpk_CONCEPT_CLASS (concept_class_id);
ALTER TABLE @cdmDatabaseSchema.RELATIONSHIP ADD CONSTRAINT xpk_RELATIONSHIP (relationship_id);

2
inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_constraints.sql
View File

@ -350,8 +350,6 @@ ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_nu
ALTER TABLE @cdmDatabaseSchema.DRUG_STRENGTH ADD CONSTRAINT fpk_DRUG_STRENGTH_denominator_unit_concept_id FOREIGN KEY (denominator_unit_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_cohort_definition_id FOREIGN KEY (cohort_definition_id) REFERENCES @cdmDatabaseSchema.COHORT (COHORT_DEFINITION_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_definition_type_concept_id FOREIGN KEY (definition_type_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);
ALTER TABLE @cdmDatabaseSchema.COHORT_DEFINITION ADD CONSTRAINT fpk_COHORT_DEFINITION_subject_concept_id FOREIGN KEY (subject_concept_id) REFERENCES @cdmDatabaseSchema.CONCEPT (CONCEPT_ID);

28
inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_ddl.sql
View File

@ -180,7 +180,7 @@ CREATE TABLE @cdmDatabaseSchema.MEASUREMENT (
unit_source_value varchar(50) NULL,
unit_source_concept_id integer NULL,
value_source_value varchar(50) NULL,
measurement_event_id bigint NULL,
measurement_event_id integer NULL,
meas_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
@ -204,7 +204,7 @@ CREATE TABLE @cdmDatabaseSchema.OBSERVATION (
unit_source_value varchar(50) NULL,
qualifier_source_value varchar(50) NULL,
value_source_value varchar(50) NULL,
observation_event_id bigint NULL,
observation_event_id integer NULL,
obs_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
@ -233,7 +233,7 @@ CREATE TABLE @cdmDatabaseSchema.NOTE (
visit_occurrence_id integer NULL,
visit_detail_id integer NULL,
note_source_value varchar(50) NULL,
note_event_id bigint NULL,
note_event_id integer NULL,
note_event_field_concept_id integer NULL );
--HINT DISTRIBUTE ON RANDOM
@ -369,8 +369,8 @@ CREATE TABLE @cdmDatabaseSchema.DRUG_ERA (
drug_era_id integer NOT NULL,
person_id integer NOT NULL,
drug_concept_id integer NOT NULL,
drug_era_start_date datetime NOT NULL,
drug_era_end_date datetime NOT NULL,
drug_era_start_date date NOT NULL,
drug_era_end_date date NOT NULL,
drug_exposure_count integer NULL,
gap_days integer NULL );
@ -381,28 +381,28 @@ CREATE TABLE @cdmDatabaseSchema.DOSE_ERA (
drug_concept_id integer NOT NULL,
unit_concept_id integer NOT NULL,
dose_value float NOT NULL,
dose_era_start_date datetime NOT NULL,
dose_era_end_date datetime NOT NULL );
dose_era_start_date date NOT NULL,
dose_era_end_date date NOT NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.CONDITION_ERA (
condition_era_id integer NOT NULL,
person_id integer NOT NULL,
condition_concept_id integer NOT NULL,
condition_era_start_date datetime NOT NULL,
condition_era_end_date datetime NOT NULL,
condition_era_start_date date NOT NULL,
condition_era_end_date date NOT NULL,
condition_occurrence_count integer NULL );
--HINT DISTRIBUTE ON KEY (person_id)
CREATE TABLE @cdmDatabaseSchema.EPISODE (
episode_id bigint NOT NULL,
person_id bigint NOT NULL,
episode_id integer NOT NULL,
person_id integer NOT NULL,
episode_concept_id integer NOT NULL,
episode_start_date date NOT NULL,
episode_start_datetime datetime NULL,
episode_end_date date NULL,
episode_end_datetime datetime NULL,
episode_parent_id bigint NULL,
episode_parent_id integer NULL,
episode_number integer NULL,
episode_object_concept_id integer NOT NULL,
episode_type_concept_id integer NOT NULL,
@ -411,8 +411,8 @@ CREATE TABLE @cdmDatabaseSchema.EPISODE (
--HINT DISTRIBUTE ON RANDOM
CREATE TABLE @cdmDatabaseSchema.EPISODE_EVENT (
episode_id bigint NOT NULL,
event_id bigint NOT NULL,
episode_id integer NOT NULL,
event_id integer NOT NULL,
episode_event_field_concept_id integer NOT NULL );
--HINT DISTRIBUTE ON RANDOM

23
rmd/cdm54.Rmd
View File

@ -19,7 +19,28 @@ library(stringr)
```
Below is the specification document for the OMOP Common Data Model, v5.4. **This is the latest version of the OMOP CDM.** Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the [forums](https://forums.ohdsi.org/) or the [github issue](https://github.com/ohdsi/CommonDataModel/issues) page.
This is the specification document for the OMOP Common Data Model, v5.4. **This is the latest version of the OMOP CDM.** Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the [forums](https://forums.ohdsi.org/) or the [github issue](https://github.com/ohdsi/CommonDataModel/issues) page.
### Current Support for CDM v5.4
The table below details which OHDSI tools support CDM v5.4. There are two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 that were not present in CDM v5.3. A green heart `r emo::ji("green heart")` indicates that the support level for the listed tool is in place, has been tested, and released. A yellow heart `r emo::ji("yellow heart")` indicates that the support level for the listed tool has been initiated but has not yet been tested and released.
<br>
|**Tool**|**Description**|**Legacy Support**|**Feature Support**|
|--|--|--|--|
|**CDM R package**|This package can be downloaded from [https://github.com/OHDSI/CommonDataModel/](https://github.com/OHDSI/CommonDataModel/). It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables. |`r emo::ji("green heart")`|`r emo::ji("green heart")`
|**Data Quality Dashboard**|This package can be downloaded from [https://github.com/OHDSI/DataQualityDashboard](https://github.com/OHDSI/DataQualityDashboard). It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study.|`r emo::ji("green heart")`| `r emo::ji("yellow heart")`
|**Achilles**|This package can be downloaded from [https://github.com/OHDSI/Achilles](https://github.com/OHDSI/Achilles), performing a set of broad database characterizations agains an OMOP CDM instance. |`r emo::ji("green heart")`|`r emo::ji("yellow heart")`
|**ARES**|This package can be downloaded from [https://github.com/OHDSI/Ares](https://github.com/OHDSI/Ares) and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research.|`r emo::ji("green heart")`|`r emo::ji("yellow heart")`
|**ATLAS**|ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. [Demo](http://atlas-demo.ohdsi.org/) |`r emo::ji("green heart")`|`r emo::ji("yellow heart")`
|**Rabbit-In-A-Hat**|This package can be downloaded from [https://github.com/OHDSI/WhiteRabbit](https://github.com/OHDSI/WhiteRabbit) and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.|`r emo::ji("green heart")`|`r emo::ji("green heart")`
|**Feature Extraction**|This package can be downloaded from [https://github.com/OHDSI/FeatureExtraction](https://github.com/OHDSI/FeatureExtraction). It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. |`r emo::ji("green heart")`|`r emo::ji("green heart")`*
|**Cohort Diagnostics**|This package can be downloaded from [https://github.com/OHDSI/CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) and is used to critically evaluate cohort phenotypes. |`r emo::ji("green heart")`|`r emo::ji("yellow heart")`
<br>
\* The **Feature Extraction** package supports all relevant new features in CDM v5.4. For example, it was decided that, from a methodological perspective, the EPISODE and EPISODE_EVENT tables should not be included to define cohort covariates because the events that make up episodes are already pulled in as potential covariates.
<br>
Looking to send us a pull request for a bug fix? Please see the [readme](https://github.com/OHDSI/CommonDataModel#readme) on the main github page.

4
rmd/cdmRPackage.rmd
View File

@ -1,6 +1,8 @@
---
title: "**CDM R Package Demo**"
output: html_document
output:
html_document:
toc: no
---
Below is an example showing two different ways the CDM R package can be used to create the tables in your environment. First, it uses the `buildRelease` function to create the DDL files on your machine. Once you have these downloaded you can then run them in your SQL client to set up the empty CDM tables. Second, the script shows the `executeDdl` function that will connect up to your SQL client directly (assuming your dbms is one of the supported dialects) and instantiate the tables through R.

23
rmd/index.Rmd
View File

@ -11,12 +11,33 @@ This website is meant to serve as a resource describing the specification of the
The current CDM version is [CDM v5.4](http://ohdsi.github.io/CommonDataModel/cdm54.html), depicted below. This CDM version was developed over the course of a year by considering requests that were sent via our [issues page](https://github.com/OHDSI/CommonDataModel/issues). The list of proposed changes was then shared with the community in multiple ways: through discussions at the weekly OHDSI Community calls, discussions with the OHDSI Steering Committee, and discussions with all potentially affected workgroups. The [final changes](http://ohdsi.github.io/CommonDataModel/cdm54Changes.html) were then delivered to the Community through a new R package designed to dynamically generate the DDLs and documentation for all supported SQL dialects.
- [Link to DDLs for CDM v5.4](https://github.com/OHDSI/CommonDataModel/tree/v5.4.0)
- [Link to DDLs for CDM v5.4](https://github.com/OHDSI/CommonDataModel/tree/v5.4.0/inst/ddl/5.4)
- [Link to ReadMe for instructions on how to use the R package](https://github.com/OHDSI/CommonDataModel/tree/master#readme)
![](images/cdm54.png)
<br>
### Current Support for CDM v5.4
The table below details which OHDSI tools support CDM v5.4. There are two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 that were not present in CDM v5.3. A green heart `r emo::ji("green heart")` indicates that the support level for the listed tool is in place, has been tested, and released. A yellow heart `r emo::ji("yellow heart")` indicates that the support level for the listed tool has been initiated but has not yet been tested and released.
<br>
|**Tool**|**Description**|**Legacy Support**|**Feature Support**|
|--|--|--|--|
|**CDM R package**|This package can be downloaded from [https://github.com/OHDSI/CommonDataModel/](https://github.com/OHDSI/CommonDataModel/). It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables. |`r emo::ji("green heart")`|`r emo::ji("green heart")`
|**Data Quality Dashboard**|This package can be downloaded from [https://github.com/OHDSI/DataQualityDashboard](https://github.com/OHDSI/DataQualityDashboard). It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study.|`r emo::ji("green heart")`| `r emo::ji("yellow heart")`
|**Achilles**|This package can be downloaded from [https://github.com/OHDSI/Achilles](https://github.com/OHDSI/Achilles), performing a set of broad database characterizations agains an OMOP CDM instance. |`r emo::ji("green heart")`|`r emo::ji("yellow heart")`
|**ARES**|This package can be downloaded from [https://github.com/OHDSI/Ares](https://github.com/OHDSI/Ares) and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research.|`r emo::ji("green heart")`|`r emo::ji("yellow heart")`
|**ATLAS**|ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. [Demo](http://atlas-demo.ohdsi.org/) |`r emo::ji("green heart")`|`r emo::ji("yellow heart")`
|**Rabbit-In-A-Hat**|This package can be downloaded from [https://github.com/OHDSI/WhiteRabbit](https://github.com/OHDSI/WhiteRabbit) and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.|`r emo::ji("green heart")`|`r emo::ji("green heart")`
|**Feature Extraction**|This package can be downloaded from [https://github.com/OHDSI/FeatureExtraction](https://github.com/OHDSI/FeatureExtraction). It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. |`r emo::ji("green heart")`|`r emo::ji("green heart")`*
|**Cohort Diagnostics**|This package can be downloaded from [https://github.com/OHDSI/CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) and is used to critically evaluate cohort phenotypes. |`r emo::ji("green heart")`|`r emo::ji("yellow heart")`
<br>
\* The **Feature Extraction** package supports all relevant new features in CDM v5.4. For example, it was decided that, from a methodological perspective, the EPISODE and EPISODE_EVENT tables should not be included to define cohort covariates because the events that make up episodes are already pulled in as potential covariates.
<br>
## The CDM Working Group
The CDM is managed by the OHDSI CDM Working Group. If you would like to join our group please fill out [this form](https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu) and check "Common Data Model" to be added to our Microsoft Teams environment. This working group endeavors to maintain the OMOP CDM as a living model by soliciting and responding to requests from the community based on use cases and research purposes. For more information on the CDM refresh process please see the description [here](http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html). You will find information on our meetings and links to join at the end of this page.

3
rmd/sqlScripts.Rmd
View File

@ -290,7 +290,8 @@ FROM @TARGET_CDMV5_SCHEMA.DRUG_EXPOSURE d
INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT_ANCESTOR ca ON ca.DESCENDANT_CONCEPT_ID = d.DRUG_CONCEPT_ID
INNER JOIN @TARGET_CDMV5_SCHEMA.CONCEPT c ON ca.ANCESTOR_CONCEPT_ID = c.CONCEPT_ID
WHERE c.DOMAIN_ID = 'Drug'
AND c.CONCEPT_CLASS_ID = 'Ingredient';
AND c.CONCEPT_CLASS_ID = 'Ingredient'
AND c.STANDARD_CONCEPT = 'S';
/* / */